The orcs. The bad guys. Are they bad because they are evil to the bone, and whatnot (take Tolkien's orcs, for instance) or are they bad just because they happen to be the good guys' enemies? That is, would killing each and every single one of them be a morally reprehensible or a morally laudable action?
Huh. That's... not an easy question to answer.
I've... largely left the orcs in the Omega-verse to be somewhat two-dimensional villains. My focus has always been on the main cast, and their challenges as opposed to going into great, sweeping detail about the galaxy at large and its various inhabitants. I consider myself very character-driven, and yes, in a way, that means that the "villains" are simply there to be villains. They're evil mostly because I need someone for my protagonists to fight against.
I suppose, then, if that's not your cup of tea, well, then it's not.
As for whether killing them all would be morally reprehnsible or the opposite... that's not something I have an easy answer for, either. I suppose I can answer that in terms of an in-universe perspective.
A lot of Confederation citizens, especially those who've been hit hard by the war are likely to say that "the only good orc is a dead orc." Sure. That's to be expected. But by the same token, a lot are going to acknowledge that yes, some horrible deeds have been perpetrated by the Dominion, but even so, is it ever right to just kill them all off?
That's where a lot of the sort of moral quandary comes from with regards to the use of biological/chemical/radiological/Macguffin-esque weapons. Is genocide ever ok? Judging by the crew's reactions, it's pretty safe to say that regardless of what the Dominion's done, and they HAVE done some pretty awful stuff, the idea of wiping out the entire race still rubs a lot of folks the wrong way.
Anywho, I'm not sure if that answered anything or just muddied the waters... it's a confusing issue, to say the least.