It's impossible to kill Yes Man, as he's a program on the network and can jump from securitron to securitron, so if you kill Mr. House, you can still go back and work for Yes Man (or NCR/Legion if you haven't pissed them off yet past the point of no return.) Regardless, Yes Man is always available if all the other faction quest lines have closed to you. And feel free to kill House. I like the BoS as well, and his demand that you wipe them out is pretty much a deal breaker for me. NCR, Legion, and Yes Man lines all require that you kill him.
Just make sure you've found all the non-DLC snowglobes before you do so though, as House's securitron Jane disappears afterwards so you can't receive payment for recovering them.