Nanoha casually confirming that she doesn't normally take prisoners
Heh.
More seriously, she's not used to people surrendering before being blasted unconscious.
how is the intergalactic government only JUST hearing about this full genocide when there's only one witch left? Who funded these guys?
Worldbuilding has never been the strength of Nanoha, and this movie continuity might abandon what few details we got from StrikerS. But the interdimensional "government", TSAB, distinguishes between Administered and Unadministered worlds. Presumably this is one of the latter, and thus not under Bureau jurisdiction or attention (the Bureau is chronically overworked.) My guess is that the UN of this planet recently asked the Bureau for help, or maybe Hayate volunteered for undisclosed reasons, but anyway information is naturally limited. Sort of like a small NATO team visiting some large African country, if we had less mass communication.
If you mean who funded the cyborgs like Zeo and Nanoha's prisoners, that would be the military of Darnaza, the particular country they're in on this planet.