There's nothing to 'get' since nobody is obligated to agree with the idea that genocide is acceptable when some very contrived conditions arise to conveniently handwave and justify it. We also know that Venat did have alternative options available to her if she truly wished to save the Ancients. She could have simply informed them of what she knew, especially since she previously claimed that she thought that 'nothing was impossible'.

Perhaps if the story really wanted us to pretend as if no other option existed then it should not have shown every other major threat be dismantled through ever escalating plot conveniences.

Attack on Titan handled the controversial subject of genocide in a much more tactful manner as far as I'm concerned. It's a real shame that FFXIV did not when it came to Venat and her actions.