Well well, I like how people bring the misconceptions about Tolkien here, this so called black and white morality is oversimplification. If anyone tried to classify it, the whole case would like mind boggling, black and grey and white it's not as simple as you think, in Tolkien's Middle Eartth there is plenty of people that are genuinely good there are loads of people morally questionable doing evil things but not classified as evil those who are good but flawed (some minor flaws or great, even those sweet, brave hobbits are mean, petty, greedy, superstitious, isolationistic and almost xenophobic in their ways but they care little for power their ambitions are limited to well fare of their families, clans, good food, peace and quiet, they are in a way anarchists but have tradition of central rule of kings, in the same time it is the head of families that are governing their own affairs and Shire has little or no government, even Frodo has flaws he has stereotyped view on race of Men, he is stern for Gollum and at first hates him, he is often foolhardy, at times reckless of course a typical hobbit traits, he is in fact a little man in great shcem of thigns, he represents an average person raising to the challenge) and those ,,good and noble" dwarves they are super greedy materialists that will remember better than you any debts or services rendered, fast in enmity, secretive in their culture and knowledge to the point of xenophobia, they too can be petty, vengeful, cruel, filled with hate and grievances and of course racism, then we have elves wiser than most peoples and yet they can be as dangerous (if not more) than all the others and then we have Men, the race of great potential and even greater affinity to be total jerks, there you have it racism and distrust (may I remind about an individual called Castamir the Usurper who owed his name as usurpator to the throne and slayer of his relatives from royal family, who started out the civil war in Gondor simply because he was a racist towards lesser men and his followers were alike, he was a cruel man whose rule was highly beneficial to the people of the coastlands as he drew resources for development of navy and he planned to make his capital at Pelargir the largest port of Numenorean origin, he was against the Eldacar the half-numenorean heir to the throne whose mother was of the Northmen the princess Vidumavi and those who pursed the pure blood policy were outraged that this half blood would ascend to the throne, of course Castamir killed Eldacar's son and the destruction his army caused ,,far exceeded the needs of war" meaning he took capital city of Osgiliath by assault and caused great slaughter and destruction) after he was killed Castamir's sons and many other rebels escaped to seize power in Umbar starting out Castamirioni dynasty and of course the opposition of later kings too sought refuge in escape to Umbar strengthening political enamies of Gondor. I think that it is not needed here to remind about history of Numenor how they became colonial empire with great ,,treasure fleets" that at first were benevolent for natives but soon their pride grew so much that they persecuted the local population (as well as treatment of Numenorean faction of Faithful who also were persecuted for a long time in Numenor itself) and this nation the Numenoreans were blessed with greatest gifts among mankind wisdom and knowledge other men couldn't hoped for, longevity, they were physically altered to be stronger and taller than any other people and with other great abilities and yet they fell to standard weaknesses of man. Then we have mentioned by many ,,but Mordor is pure evil" well what is Mordor? It's a land, base of operations and it earned bad fame which is understandable, from there hordes o merciless invadors come to pillage and burn, dark creatures, bred monsters and works of sorcery come from there, but it is also something more, military base with proper order where each army unit is pushed into place like pawns on board a great chessboard in the mind of it's sole unquestionable ruler. There are mines and forges there, fortifications, armouries, walls and strongholds, net of well made roads for easy communication and transport, each orc has number and rank and there is clear chain of command, there are whole shanty towns of huts and drab buildings of Men and Orcs, there are fertile fields and thousands of slaves working, tunnels and caves, fortified military camps a la ancient Rome (black and red tents set in order or buildings surrounded by defensive walls with whole streets bustling with activity, it's a vision of order in the mind of it's sole guiding force, because this is Sauron's purpose power and new order according to his designs, power over minds of sentient beings with their independent wills (he likes riches too why he demended from orcs that plundered Moria tribute in mithril or why there are whole wagon trains of goods, booty, fresh slaves and tributes from conquered or tributay lands of his vast empire in the East and South, of course orcs still can be a bit unruly especially if they come from breeds of more or less independent tribes and clans that serve unwillingly in wars of the Dark Lord, or whne he overdoes it with magically filling them with hate adn fury to fight better hehe, but the iron rule of ,,god-king" Sauron puts them quickly in place
in fact Tolkien writes that he started out as all tyrants do, from the benevolent notions of improving the lives of sentient beings on Arda, ,,nothing is evil in the beginning even Sauron was not so")
Now to the Nilfgaard we go, as for possibility of joining with it I rather doubt that. First of all from what I read about Witcher 3 it will be more personal story so it wouldn't be a great surprise if any world shattering policies going on (and the invasion in progress) would be rather less important than personal pursuits of Geralt, as for his attitude towards the emperor as he already regained memory he would know exactly what Emhyr did and why and as we see in The Baptism of Fire he clearly disaproved the Nilfgaardian ways (which I will cite again from other work of fiction ,,far exceeded the needs of war"
) even during his talk with Fulko Artevelde there is this personal attitude towards empire adn it's internal workings (Geralt does not hesitate to accordinlgy judge what he sees, he saw the nilfgaardian colonists being resettled in Northern Kingdoms after the war and he clearly despised their cruel treatment, in fact Dandelion reminded him to not get himself involved thinking that he would intervene, so he was critical towards Nordlings too, he is cynical but he sees in his mind what's wrong and what's not, so I would not rule this out, after all we have a set character to play as and thought some freedoms are for the players it would be a bit non-character to assume that Geralt just like that would suddenly be freinds with Emhyr). Geralt at one point claimed that he would work for nilfgaardians to protect nilfgaardian children for money at the ruins of the world if he had to, but that in my opinion was simply his stance of neutrality being brought up to discourage Triss trying to involve him in conflict (Blood of Elves), Triss if I remember too had critical attitude towards empire adn the destruciton and suffering the war brought to the people (and not simply because she fought against them on Sodden hill or that her position as sorceress in Nilfgaard would be compromised, she tells that consumed by fear she knew no more whether she fought for interests of mages or policies of kings, she despised her moment of cowardice but she tells Geralt that they the fourteen from Sodden Hill stood there because it was right thing to do). Geralt also isn't a great hero but he is more noble than he thinks himself, why when Ciri tells that she would stand with Triss to fight he rebuts that she will stop learning the sword fight unless she'll understand what sword means in witcher's hand. Moral relativity of our times is astounding sometimes, are we to justify the cruelty and evil because...it's complicated and nothing is purely good or bad?!