I don't necessarily think the "reset" of the future (and thus, the past), the culmination of September and Walter's plan, will eliminate the Observers altogether. Rather, it may set them on a different, more benign path. (Eliminating the Observers would also eliminate September and the whole plan, no? Yeah, makes my head hurt too, as Captain Janeway once said.)
Once Michael "returns" to the future and shows those advanced scientists that they don't have to remove emotions from the human brain to achieve advanced intelligence, the Observers may evolve into a different, more benevolent species - the culmination of mankind's evolution that we all hope for. Not only will the horrors of the Observer invasion be avoided in our
time, the future will be one of peace, harmony, and universal prosperity. Talk about ending the series on a high note, eh?