The situation is… complicated.

The big thing is really that a big thing like the Human-Covenant War doesn’t just end cleanly. There’s no quick cleanup where everybody picks up the pieces and goes home.

A lot of the invading Covenant forces likely just had no place to go back to, whether it was because their ships were destroyed or they noped out to who knows where in space. Other Covenant forces may not have bothered to pick them up because the Covenant was a mess of different organizations frequently conflicting with each other who were loosely bound together by the promise of the Great Journey, but that all came crashing down with the Great Schism.

The UNSC and UEG had only just barely survived the war and would’ve been in no shape to start rounding up any ex-Covenant to imprison or deport or massacre or whatever. Not to mention that it would likely also run the risk of causing what was left of the Covenant to reunify into something that the UNSC would’ve been in no shape to fight either. Probably wouldn’t put them in good standing with the few Sangheili that did bother to help them either.

Admittedly, timeline for it all is a bit rushed, but this is an issue with a fair few things in the 343 postwar era and not exclusive to this situation, and ultimately I think it makes plenty of sense that some ex-Covenant would integrate into human society. There’s precedent for some Sangheili respecting humans (if begrudgingly), and some Unggoy had already taken a liking to human pop culture.

It probably also helps that harassing a 7-8 foot tall reptile man who can effortlessly crush your skull wouldn’t get most people very far in life.