This is my first playthough siding with Yes Man, I have killed house and uploaded Yes Man into the computer. He said I needed to make contact, So I made contact with the BOS and went back to Yes Man. The only option it gives me is to keep them alive, but I want to kill them. Is there away to do so?

Yes.

By killing them.

Buy GMG
load pulse rounds
Kill Spacemarines
And then cook for ten minutes.

I can't tell Yes Man to wipe them out?