This is THE most difficult question.
On one hand, if a species is capable of free will, then it's just outright not right to do it. On the other hand, if they cannot be communicated with and they are relentlessly pursuing your species' destruction and will bounce back with even more powerful weapons if you defeat them and leave even a few of them alive, then really, there's not really anything else you CAN do.
A race would have to be cartoonishly evil and purely devoted for it to be even remotely something on the table, or just plain unable to understand the value of life while spreading like a virus (So, like actual viruses). Like, I'm sure even the Orcs of Tolkien could find some form of balance. Hell, some Draconians managed it in the Dragonlance books, and that was kind of amazing. On the other hand, the X Parasites from Metroid Fusion? Yeah, no. No you can't negotiate or deal with that.
Oh, and on that note, just one last thing to throw in here. If Metroid Fusion showed us anything, it's that you should be REALLY careful about completely eradicating a species. You don't know if it's suppressing something far, FAR worse that DEFINITELY needs eradicating if it gets out of hand. ;>_>