The answer is, "You, the reader." Your view of right and wrong is what is important, not what the gods decide. A lot of what happens in OOTS seems designed to provoke the reader into thinking about what makes someone a good guy or a bad guy--and it's not whether or not they're a god or a paladin or a goblin.
Whoa, whoa, whoa. Back it up. Thor has never sanctioned any such thing, and has no power over what the Twelve Gods do with their followers. And we have only tentative data on how much Thor was involved in the creation of the fodder races to begin with, or what rules he might set down for his followers when dealing with them.
It's pretty easy if you have no faith in the authority of gods in the first place.
Except Roy isn't trying to oppress the goblins; they don't even really figure into his decision-making. Roy is trying to stop Xykon, and that is pretty much guaranteed to be the right thing to do. The interesting thing will be to see how Roy deals with Redcloak and his people after Xykon is defeated (assuming Redcloak is still alive at that point).