the reason why its also confusing me is because if you choose yes man then the ncr wont support you anymore (dont tread on the bear) and to me so far in the game the NCR are the good guys......but whatever, i guess i'll just play it out and see what happens but i do NOT want to kill NCR people....
You do NOT have to kill ANY NCR with House or Yes Man as long as you have 100 speech (and arguably a good sneak for one of the missions). Otherwise at end game you will be forced into conflict with a few (literally, 5 I think?) NCR members. You do not have to kill them yourself but their deaths are unavoidable without the 100 speech (magazine usage is possible as long as you use it before entering dialogue)
As for why, they're not perfect by any means. They want to use the courier as much as anyone else, siding with someone other than them puts you on their black list. Put it this way, if you do the NCR run you have to assassinate House. They don't like him (or Yes Man, but they don't know about him till the very end).
Also, disconnecting House is a fate far worse than death. Seriously, it's a horribly cruel thing to do, if you want the best path morally when it comes to it, kill House, don't just leave him to slowly die...it's a horrible way to go.
Of course, NV is too grey to allow any one path to be best, this is purposeful, obviously. It also leads to some interesting endings...