I just finished the quest, acquiring the Presidential Suite. However, this seems to lead into a quest which would have me take over Vegas, which is clearly intended for "bad karma" characters. I want my character to follow the "good" path in the game. How should I end the quest?

You're being presumptuous. The Courier taking over Vegas is the nicest ending, since everyone else are big meanie heads.

Pick whatever you like the most. NCR, Legion, House, or yourself.