Maybe, and that's final.
No really, morality is in the specifics... the circumstances. For instance it's one thing to kill someone who is trying to murder you, and quite another to subdue them and then kill them (that's murder).
If the bad guys attack the heroes en route to reclaim a lost relic, killing the bad guys would most likely be self defense.
You can also go with the idea that "things are different" in the setting as someone said above. Society might be fine with you for killing a bunch of kobolds. They may see kobolds the way that colonists saw the Indians or wolves... dangerous pests. Maybe the gods of good see wiping out villages as the greater good. But does that conform with the idea of goodness?
i believe it doesn't. Seeing kobolds as dangerous pests is neutral at best, im<ho. To me, being good involves mercy, compassion... traits that make us vulnerable, but make life worth living. Good PCs should go to great lengths to avoid murder. Laying waste to a goblin village is likely murder.
A solution might be to abandon alignment. Instead, let society judge them as ours does. Or let each deity judge. Each deity would have its own moral code. Pelor might frown on killing kobolds needlessly. A warrior god might see it as good exercise.
If you want a more interesting game... challenge this issue/thinking. Are the goblins evil or desperate? Meaning, are they looking for an easy living by stealing what others have earned or are they somehow unable to fend for themselves and are stealing food to feed their children? Start the story with something typical, cut and dry like "the goblins are raiding shipments". Then when the PCs investigate they might find that the orcs have displaced the goblins or are forcing them into it. Now things are tricky. The players might realize, "if my kids were starving I'd consider stealing" or "if my kids were held hostage, I'd do ANYTHING to save them". What started as clear and simple (and boring) has become complicated and conflicting (interesting).
It might also depend on how you think of free will in the setting. Are drow evil because their spirits are formed my Lolth? Are they genetically disposed to being evil? Are they beaten into submission by their matrons, mocked for showing mercy? Would being less than evil mean death or being at a severe disadvantage? Maybe the environment is so hostile that goodness is a luxury the society can't afford. Look around today and you'll see this thinking.
It matters because if the drow are redeemable, killing them becomes tricky. If they are inherently evil... let the bodies hit the floor.
Though, some players will prefer a more traditional "us vs. them" and "red beady eyes == kill them all". Sound like anyone you know from the real world?
If you really want to dig into it, run a game where the PCs are kobolds or goblins or orcs. Add some stats for hunger and pecking order. See what the PCs do when they are bullied by bigger orcs and they are starving. Make them drow and put them in a society that sees good as evil and vice versa.
Another way to making things interesting is to have all humans. That way the characters and players might see themselves in their enemies. Or just decide they don't care.
