The issue with this is that the game doesn't really communicate this fact to you, and not killing the goons technically should mean that they're still going to go upstairs at some point and kill Paul.
The most hilarious part of this is that Paul himself says he's too weak to climb through the window, but as soon as those goons bust in through the front door, he whips out a 50 lb flame thrower and starts strafing around at 30 mph like he's in the motherfucking murder olympics.
You can kill Anna on the plane where you're supposed to kill Lebedev; the game accounts for this with voice dialogue and everything. Crazy. At that point in the game there is no reason for you to even try (and she's a tough match) unlike later on --- but you can!