How about letting hundreds of civilians burn alive so a merc can get revenge on a petty warlord?
If you chose to interprest it that way then yes, it's evil. On the other hand, this petty warlord has shown that he is perfectly happy to kill those civilians. If he's allowed to live, chances are he will kill many more. Thus by sacrificing the people in the refinery, you likely save more lives in the long run.
Regarding the genophage, everything we know about the krogan says, once recovered, they'll launch further war, with billions upon billions more caustalies. Curing it is the evil option, as it would unleash that upon the galaxy. And even if not doing so involves betraying a friend, that changes nothing. Anyone who would put personal loyalties above the lives of others cannot be considered good.