I don't know, I feel like the two 'evil' men aren't really comparable in a lot of ways, and neither was their actions.
First of all, on a personal level from the perspectives of the PC and Alistair, their acts are on a different scale. Duncan didn't raise Alistair, and given that he's a new recruit himself, how long could they have really known each other? A month? A year? Howe, a family 'friend', directly attacks and kills your family .. father, mother, nephew, sister-in-Law, all your friends, and everyone that helped raise you .. out of sheer greed. And lets not forget, as I think someone was pointing out already - as far as the PC is concerned, Loghain is the reason your brother is dead. So you have easliy as much reason to hate Loghain as Alistair does.
Secondly, I'm not sure I agree with everyone making Loghain out to be pure evil. His actions don't seem to be motivated by personal gain, but rather a paranoid delusion. And his delusion isn't totally unfounded. He clearly suffered greatly under Orlesian rule, and risked everything to drive them out. It's no doubt what he views as his greatest achievement. Now, just 30 years later, Maric is dead and his inexperienced son is allowing Orlesian troops to waltz into a weakened Ferelden. At the start of the game, it really isn't all that paranoid to suspect that the Orleasians would take advantage of this unproven 'blight' by waiting for Ferelden's forces to be weak and unorganized, then take over once again. As the game progresses, however, it becomes clear that his plan isn't working the way he wanted it to, and that the blight is in fact real. But its too late, he's committed to his actions, and it's probably his growing desperation that leads him to his most heinous acts, such as selling slaves (probably Howe's idea). Recall how upset he seems when Howe brings in Zevran? Obviously hiring an assasin goes against some set of morality he still wants to cling to.
Regardless of origin, it still would bother me as the PC to let Loghain join the wardens. Even if he 'meant' the best for Ferelden, he clearly went too far, he sacrificed way too much morality. However, it wouldn't bother me so much that I'd just give up and walk away. Alistair's reaction does seem too extreme to me, and I lost a fair amount of respect for his character after seeing that the first time. It also bothers me b/c it's out of nowhere. We really don't hear a lot of animosity toward Loghain from him throughout the game- a little but not much. Mostly he's just this goofy guy, a comic relief type, not at all dark and brooding and bent on revenge.