The problem is that the game actively punishes you for not liking Johnny and antagonizing him.
Both playstyles, working with him, or seeing him as a threat and working against him, should be equally viable. Instead rejecting him whenever possible puts you on the road towards the Arasaka ending and we know how that plays out.
The real Johnny Silverhand died in 2023 and trying to save your life, while not listening to the digital malware that came out of Mikoshi, should have led to a better ending. Instead V gets painted as a coward and corporate sellout.