That's why it's not a jury, but a committee of some kind. This is literally their job. Also, as I pointed out in another thread:
We've never seen the full text of the Prime Directive anyway. That could easily have qualifiers.
Also in all cases theres a reason you need a committee to vet PD violations: Laws are bad at accounting for edge cases, and PD violations are almost always edge cases. Fixed exceptions encourage people to warp the situation to fit the fixed exception.
The committee allows for a nuanced judgement, where not just the Why, but the How matters:
-Wholly justified - E.g. Prime Directive violated in the process of stopping a warp capable species from using a prewarp planet as a slave pinata, accomplished without being observed.
Captain gets off clean, may have a meritorious note.
-Justified, but improper execution - E.g. Prime Directive violated in the process of stopping a warp capable species from using a prewarp planet as a slave pinata, however, leading to an open firefight on the planet and significantly deviating the native culture.
Captain is censured, not because they did wrong, but because it needs to be made clear to take all possible efforts not to impact local culture.
-Weak justification, but executed well - E.g. Two prewarp sophont species engaged in a war of annihilation. Action taken to avoid extinction, defeated party evacuated from the planet and settled onto another.
What we have here. The justification is really problematic here, because aside from genetic differences the situation is pretty much identical to a species committed genocide on a subspecies/subrace of itself, and THAT is expressedly forbidden to intervene in.
I expect captain to keep his hat and chair, but be censured.