Question: Did they give John Lithgow's character Alzheimer's disease in remembrance of Charlton Heston?
Chosen answer: No they most certainly did not. That wouldn't remotely be considered a particularly respectful homage! They picked Alzheimers because it's specifically a brain condition, which can then be explored in the movie as a plausible way of explaining the intelligence raising properties of the drug used.
Question: Why did Juni leave the OSS again? Also, why does Carmen seem to hate him again? They got over that in the first movie.
Answer: He retired from the OSS. Carmen hates Juni because after he went out on his own he never called or did anything to let her know where he was or how he was doing.
Answer: He considers Hunt to be a friend, so did what he asked. In addition, by carrying out the deal he has ingratiated himself with Sidorov as well.