If humanity gets nearly wiped out, (down to less than a billion, heck, even down into the tens of millions,) their continued survival depends a lot on how they went down.
If they went down fighting this ancient evil for the good of the galaxy, after being the only race that heeded the warnings and prepared? I don't think the rest of the galaxy will abandon them to die out. I honestly don't. The rest of the galaxy didn't wipe out the Krogan, and they bombarded Turian colony worlds with meteors from orbit, essentially killing everyone there and salting the earth so that nothing could ever grow again.
The Quarians are an unpopular nomad race largely because they got decimated by their own mismanagement, rather than by an outside force, and because it's really hard for them to find new colony worlds. There's Garrus and Tali dialogue to that effect in ME1 (also: ME1 Garrus is kind of a dick.)
If humanity got nearly wiped out in a war with the Batarians, then yes, I think they'd be pretty screwed. Wiped out in a war with an aggressive, unpopular race... a war that, if it proceeds, most alliance races will feel we started? If that happened, we'd essentially end up like the Quarians, which I do not want to contemplate.
But humanity with a population of around a billion, a newfound chip on our shoulder, and a huge reputation as a hero race? I like our odds, then. I honestly think this might be something like this might be the "Paragon" ending of ME3, where we're hurt but beloved throughout the galaxy, ready to make our way as equals, prophets, and heroes.
I think the "Renegade" ending would have us suffering a lot fewer losses, but at the expense of screwing over a lot of other races. So we'll end the game with 10 billion or so humans still in the galaxy, but a reputation for destroying Mass Relays that wipe out colony worlds, and using horrible tactics to ensure our own survival: strong, but with a terrible uphill political battle if we ever want peace.