at least the humans aren't holier-than-thou hypocrites to boot.
Unless their name is Karl Agathon.
He out-Cyloned the Cylons!

Well we all need to have goals.
But I didn't count it against him because the way I see it, he was siding with the mother of his children against his own species. Yet being able to breed with another being means she
is your own species. Richard Dawkins would be the first to understand why Helo would selectively defend the Cylons at the expense of humans. The mother of his future children is not a human, therefore the investment you'd usually expect a human to have in other humans has gone missing.
What I don't buy is that any of it has anything to do with morality. It's just primeval instinct.
As far as the BSG genocide debate goes, the short version of my opinion is Helo did the right thing ethically but not the right thing practically, and I would definitely have done the latter (as savagely immoral as I concede to consider it).
Oh yarg I'm being sucked back into the BSG Battle.

You're right, given what the characters knew, not what the audience knew, Helo's actions were completely insane.
You have a bunch of killer robots trying to exterminate humanity. There is one and only one rational response: exterminate them first. To hell with morality. In a pure survival situation, it doesn't apply.
The characters should be let off the hook because they had no way of knowing they were in the middle of a badly written plotline, where the murderous nature of the Cylons hinged entirely on the insanity of one of their tribe and the gullibility of the rest. But even if they knew, would you bet the survival of your species on a bunch of robots who are either insane or stupid? I sure wouldn't.
All that is at a societal level. If your loyalty is still to a species at that level, it applies. Helo's ability to breed with a Cylon had severed that loyalty and transferred it to where his genes would be most likely to be propagated in the future - the Cylon species. Interbreeding makes the issue of who is what species moot. And I guess he isn't too worried about stupidity/gullibility being inherited traits on the maternal side.
Personally, I'd have exterminated the Cylons. But I would have preferred to exterminate the idiotic plotline and re-written the whole thing from the ground up so that it didn't hinge on inanities. It's impossible to parse the morality of a plotline that wasn't thought through to begin with, and got mangled and mashed just to try to create a coherent narrative after the fact.