There's a logical fallacy at work since if he trusted you with a cold generator, you'd probably also want him to know.
Look, I have feelings on Thawne that mostly add up to me thinking he'd look great as a frozen sculpture forever. And Barry seems to be Barry and not brainwashed or love spelled or enthralled or some other thing, so he says you and him and Iris are a thing I'm just going to be confused but accept it as a truth based in a not entirely logical universe.
So yeah. I'll freeze you up. But not in secret from Barry and since if you're on Team Flash, you have to actually play by good guy rules even though Thawne doesn't, which means he can't be dead. Just really really freezer popped.