I don't think it really matters that Hydaelyn isn't trying to actively kill our character or the Scions. If they're honest about their lines in the sand regarding morality, then they should be disgusted by the idea of genocide aimed not only at themselves but other groups even if they stand to indirectly benefit.
I'll showcase this lovely panel from a certain manga that recently concluded and dealt with similar themes:
We have a very large cast of characters in this game. The idea that not a single one of them could be fiercely opposed and angered by the knowledge of what Venat did feels like a stretch.
It also isn't mutually exclusive. A character can be thankful that a serial killer pushed them out of the way of an incoming train but also be disgusted by the fact that the serial killer is...well, a serial killer.
This is how things operate with Emet-Selch. At various points, they're thankful for the aid he provides in terms of reviving Y'shtola or offering up valuable information. Yet they never forget or pretend as if lacks a lot of blood on his hands.
I don't think it's unreasonable to expect Venat to be treated similarly with all that in mind.