I mean...

They're more likely to be hybrids instead of a real species. They have dental traces of both near sapian cousins and only found in waaaaaay more ancestral cousins.

With hybrids it's actually kind of common for males to abort before birth. Something about the mothers immune reaction to the y chromosome or something, I'm going off memory.

But it could also explain why that group of hybrids lived alone.

A hypothetical reason for why human/neanderthal hybrids tended to be born to human mothers, was neanderthals developed faster. So to a neanderthal mother, a hybrid appeared to have developmental delays mentally while also being a weakling and never lived to reach its intellectual peak.

Meanwhile a hybrid raised among humans would develop physically faster and always be stronger, but also develop mentally faster, even if not peaking as high.

It's possible that Naledi may have only been capable of reproducing females from one or both origin species. Or even been a neutral (possibly sterile) group between the two origin species where hybrids (always female) were abandoned to be raised but what may have been outcasts.

Like, we honestly can't even say they're a unique species and we've been off by a lot more before.

Scientifically its important to analyse it, but I understand that at a certain point it becomes grave robbery.

I feel like 10,000 years is a pretty safe line...

That's never stopped archaeologists before for human cultures either

The other conclusion is a genetic modification that makes our test for “male” not work on them.

Which is also posited in the article.

why would species have anything whatsoever to do with this? Everyone deserves respect regardless, obviously.

IMO the ideal is to just leave things be if we're confident it won't be disturbed (this is both respectful and means we can use better methods to study it in the future), and if we're not confident then we extract things and preserve them in as respectful a manner as possible.
Don't disturb more than necessary, have people perform whatever rituals they feel are suitable, and if at all possible restore the site as close as possible to how it was (but making sure it won't degrade).