Suspension of disbelief is on a sliding scale. Sure if they tried to say Keyes survived getting floodified then having his brain caved in by the Chief's fist, that would require a hellofa good explanation and a lot more effort than saying "Jorge survived because the ship remained intact and exited Slipspace on the system's edge and he was picked up by an ONI prowler doing damage assessment".

Of course until that's made official, its better to assume he's dead based on how it was presented in game, but until we see a body, he's Schrodinger's Spartan.