We don't take pills through the whole game. Everyone thought this would be a action we'd be doing. Again, all of a sudden this matters. You have to be consistent in the whole game for this to work.
I understand what you are saying but I am looking at things from the narrative as it is presented. There are a number of plot holes that could be discussed. But when the don’t fear the reaper mission starts it’s right after Johnny took control of V’s body and brought V back to the ripper doc. Unlike the other endings there is no recover time for V nor does V take the pills to either suppress V’s consciousness or Johnny’s. V and Johnny just head strait to Arasaka they don’t even take time to gear up. V goes in with whatever gear V had on them at the time of the Embers meeting
Then we find out that relic has changed V’s dna later on. So, given all that information from the narrative I tend to conclude that V’s health is in a really unstable state during that mission. Both V’s body and brain has been altered by the relic so V’s unstable in the ability to control their actions. Which I think is part of the reason during the mission there is so many relic malfunctions, the relic is trying to flush what’s left of V’s consciousness out. The medication as presented in the narrative is a mechanism for V to regain control or option to give control to Johnny in a temporary manner. It doesn’t seem to be a long-term solution and given what Alt said at the end for even the small number of times it was used it accelerated the relic process to the point where if V chooses to keep the body they would only have 6 months to live.