Of course he is doing for Eddie (helping him to reach his full potential and fate), but that doesn't mean that Eddie has to be linked to the speed force.
If Eddie is Malcolm Thawne / Cobalt Blue, a villain not linked to the speedforce, then what Eobard Thawne did to him is pretty logical :
Malcolm Thawne is supposed to be "the first Thawne, the birth of the evil branch of the family". Eobard said that, for every "past" people he met, he improved their life. What if, in the original timeline, Eddie wasn't the brillant cop, but the simple janitor of the police station (like Malcolm Thawne in the comics)
By improving Eddie's life, Eobard has put his birth in jeopardy, if Eddie is now happy and will marry a woman (Iris) that is not Eobard ancestor. He so wouldn't have any reason to become a villain but, worst, Eobard won't be conceived. It's as dangerous for him as Eddie getting killed now.
So Eobard has to "correct" this. For the first time (I may be wrong, but that's an impression), I had the feeling that Eobard lied or hide something when he said "you're a failure and the only forgotten Thawne". When he spoke to Cisco "before his death" or in the last episode with Eddie, Eobard seemed totally honest with his revelation about the future. I had the feeling that it wasn't the case this time. (Awesome acting from Tom Cavanaugh if I'm not mistaken)
By revealing that Eddie "is a failure who won't marry Iris", he not only insure his own birth, but, if Eddie is Malcolm Thawne / Cobalt Blue, he also push him to the "right" direction of his destiny, insuring his future villainy, but he also give him Malcolm greatest power in the comic : The jealousy against Barry that trigger his blue flame. like Eobard always says : "A mean to an end". He is probably not happy to do this to Eddie, but he needs to do it.