Actually, I believe Eddie Thawne=Eobard Thawne, at least far as this show goes. In that I don't believe they'll have Eddie Thawne be really Malcom Thawne and Barry's long lost twin, or have Harrison Wells be a descendant of Eddie Thawne or something like that. Rather, after this episode, I'm thinking the following:
Harrison Wells is a Reverse Flash, but not THE Reverse Flash. He's only pretending to be a part of his whole M.O. to motivate Barry into increasing his speed/becoming the Flash, etc., pretty much the same M.O. as Hunter Zolomon in the comics. (Not to mention that, seeing how the suit appeared to be powered by Tachyon particles, that also fits in that Zolomon's "super-speed" was actually time manipulation). The real Reverse Flash, I think, is a older, future version of Eddie Thawne, hence why the Reverse Flash in this episode didn't kill him, either because Wells knows Thawne has to live in order for the space-time continuum to remain intact, or, if the Reverse Flash was actually the future Thawne in that scene, he obviously can't kill himself.