I think, PERSONALLY, that once you start using console commands to directly affect the outcome of events in the game then you might as well either stop playing or just turn on God Mode and have done with it.
I suppose if you can rationalise it but to be honest I would think it destroy the sense of immersion.
I agree with Phon. I'm on 360, and sometimes I keep that guy alive, and sometimes not. It's part of the current play. I've made over 20 full characters, long-term characters. Some of their stories are great, some are tragic..... the possibility of having nothing go your way (in terms of the randomness factor) makes playing fun. If I knew what the outcome was every time, why play?
Baurus, Jauffre and company have only survived once, doing the MQ. I stll keep trying to keep them alive, if I do the MQ that is..... I KNOW what is going to happen during the final Oblivon crisis. I KNOW what the final outcome will be. What I DON'T KNOW is what the journey will be like. <<<----It's this, that I enjoy.