From the final cinematic, Kerrigan is not completely free of Zerg "infestation". Her hair is still a mass of cilia-like spikes. However, I think she is now in control of her own mind, instead of being driven by Overmind implanted directives and such. But now, there is a power vacuum within the Zerg ranks, with no prime intelligence to direct the Zerg. Samir Duran will step in.

I think HotS will be about Kerrigan trying to bring the Zerg under Terran control or alliance with Samir Duran finally revealing himself to be the Fallen One's puppet and mastermind behind the hybrids.

As for the Overmind, I don't think it is a retcon to make it want to be free of its Xel'naga overseer (Fallen One? we don't know yet). It is perfectly reasonable that it had a greater plan for Kerrigan, but it did not anticipate the human condition [for personal freedom and ambition] leading her to betray the Overmind. I think the reason why the Overmind made a Zerg/human hybrid out of Kerrigan was because she would then be outside of Xel'naga influence, as humans are not their creation.

P.S. Where did you hear the 18 month estimate? I hoped it wouldn't be a yearly release, as that is just f***ing stupid. Although, they haven't started on the expansion. grrr