In that case, they could have handled over her to the Klingons.I do agree with the majority of what you say here but disagree on execution for the war crimes - the UFP shouldn't have the death penalty (think the presence of it in TOS was simply an element of when it was produced - far fewer supported it by the time of TNG and certainly now which seems to be reflected by the fact it isn't mentioned again) by that point in my opinion.
I'm also of the view that the taking of a life as punishment does not correct for having the person having taken a life themselves - although I do not judge anyone for feeling otherwise as I don't know how I'd feel were it someone close to me who was killed - so would prefer something other than that (most likely indefinite incarceration - how can you give a life sentence to a being who would likely outlive generations of people after the fact?).
This is what is meant to make Seven's summary execution of Bejayzal so hard hitting (in my opinion) is that what this person has done to a beloved character is so severe that it has driven them to such lengths - although I caveat that with not knowing what rules the Fenris Rangers operate under and so Seven might have had the right to do so in that particular instance
If she could live for centuries, who would know what would happen if she got loose again and started over with her genocide politics.
It would be like having an immortal Hitler released from prison.