I'm breaking my "never respond to you" mantra because this is so important to say.
I wholeheartedly reject the premise that "justice" for murder can only exist if the perpetrator is killed. I cannot state this strongly enough.
The flaw in your concept here is that the Perpetrator isn't a sentient being. Its a like giant space shark that has killed hundreds of thousands, possibly even millions, already and will continue to do so, as that is its nature and what it does. To paraphrase Jaws, "Its miracle of evolution, as all it does is float around, eat entire worlds, and make baby sharks". The CE is more deadly than the Borg, as the Borg usually leave the planets intact. The worlds are barren wastelands after the CE comes through. You aren't going to reform this creature. At best they would have been able to send it to another area of space to be someone else's problem. It needed to be destroyed, to do otherwise, would have been a dishonored to the memory of those that it had already killed.