I think the end-game of Mass Effect (1) did a good job of good versus evil where evil is a plausible non-psycho choice. You can save the council and allied fleets by (essentially) sacrificing the Human fleet. It's not fully good vs evil, of course, as both get the job done. But as someone working for the Council, your employer is a stabilizing force within the galaxy. It's far from perfect, but it's better than Krogans nuking everyone. While the council didn't believe you about the Reapers (which was largely just written poorly) they'd have to believe you after a reaper just about impregnates their space station, right? So the optimistic boy scout choice is to the save the (hopefully reformable) institution.

I waxed those weird looking xenos. Remember Shanxi, mothers! Keeping the human fleet intact seems like a good idea since most of the aliens already hate our upstart guts, and a human council will work to protect our colonies.

It doesn't work out in ME2, but what can you do?