Does God have free will? You're not making any sense.
An omnipotent being can do anything. Wouldn't be omnipotent otherwise.
That means an omnipotent being has the power to cease to be omnipotent.
That's all the stone case illustrates. There isn't the beginning of a problem here.
Here's an analogy to illustrate the very confused way you think. Bachelors don't have wives. Does that mean that bachelors are unable to have wives? That, if you are a bachelor, there is a strange cosmic force preventing you from marrying?
No, clearly a bachelor 'can' marry. It is just that upon marrying, the person of the bachelor will cease to qualify as a bachelor.
So, bachelors do not have wives, but they have the ability to have them.
Similarly, an omnipotent being has the ability to create a rock she cannot lift. Were she to do so, she would cease to be omnipotent - indeed, she'd be making herself less than omnipotent as the means by which to create the rock, for until she makes herself less than omnipotent, there will be no rock she cannot lift.
Anyway, the moral of all this is that you're very confused.