Yes, I'm sure it will end up being fine that Kerrigan was turned human. It's a game. Of course it will all work out.
The problem is that it's not rational in any way. If someone told me that there was one soldier who could beat and enemy army and he had to live. I sure as heck wouldn't chop the guy's arms and legs off and say "but he's still alive" when the enemy army slaughters me. It's just common sense.
I actually don't understand the point anyway. Didn't they basically hammer home that Kerrigan had free will even as the Queen of Blades? In SC the cerebrets were ticked at her seeming insubordination to the overmind. In the vision from Tasadar he said that the overmind created her to be the savior. She should have been acting with freewill already apparently.
As far as we know neither Valerian nor Arcturus had enough knowledge to be the sole influence behind Tychus. So, either they're working together master minding the whole thing or someone wrote a plothole filled story.
The secret missions were interesting. We've yet to see them payoff though. It's easy to create a puzzle and let the player think of a cool payoff. It's harder to actually come up with a cool payoff that everyone enjoys.