Well then! Since you're so stone-set on the Nomads being intelligent beings, whats to say they don't have pride? I mean, they nuked our sun. "Great success!" 800 years later, we annihilate their entire armada/army (since technically they are in and of themselves ships and creatures). Wouldn't you think they'd be a bit prideful to just surrender to these... Abominations they so sought to destroy?
That would be similar to the middle-eastern extremists throwing down arms and saying, "We've had too much fighting! You've only killed thousands of us, but we're done now! Plleeeaaase? Alliance? Friends? Yes?"