Is being unanswerable really so terrible even if lives are saved by their actions?
Yes, it is. There must always be accountability, and oversight, and the chain of command. There must be order.
Without that, there is chaos.
And is it possible to commit genocide against the Founders? If they're in the Great Link, aren't they just one individual?
If they were, then they couldn't even separate in the first place.
It seems clear that the Founders are indeed a race of separate beings, who can temporarily combine into one for the purposes of the Link. But the fact remains that they are still a species.