Im currently playing through the NCR questline.
Once I finish, will it be possible to switch over to Legion, and kill the NCR once I've done their story line?
Yes even if you pick the save from before the point of no Return IRC that's the mission after you enlist Boomers the ending woud be lacking if you're not started to back up one of chief four factions from the very begining. At least FNV force to you to RP for a change.