What do lab researchers generally do with a cell culture that's deviated from experimental protocols?
See what happens?
Seriously though, sapient species are another matter entirely, especially if they're immediately capable of joining the Summed Psyche.
Sapient species never seem to stop declaring their huge uniqueness and value. One could conclude they are a tad self-centered. One even might conclude they are a tad dangerous for that reason alone.
Not so much uniqueness as distinction. And it doesn't stop at sapient, either: an entity like the Vishnans has similar, perhaps even far greater consideration.
A sapient entity has the capacity to truly understand and learn things that are entirely outside their experience or proximity. That capability means that it is effectively more practical/efficient to teach a sapient entity (that is willing to learn, even if that willingness comes as a result of an ultimatum) the 'problem'--be it their problem, some universal problem, some abstract problem with major consequences for other entities, etc--and encourage, enact, or enforce a solution, rather than wholesale or even callous slaughter.
The Vishnans sort of do this themselves--the big discrepancy is that they seem to arbitrarily distinguish between 'okay' and 'not okay' ways of intervention, manipulation, or guidance, and when things don't go exactly according to plan...kill everyone (?).
At least when it comes to the Shivans, their goals/criteria/protocols don't involve such a dynamic at all--they kill any race that doesn't meet its specific, strict criteria, and they don't manipulate races towards those criteria (at least not that we know of).