If the NFL tried to stop Kroenke in substantive way, be it punishment or taking over the franchise, just because he wanted to move and the NFL said no and he did it anyway, it would absolutely be a lawsuit. And Kroenke would almost certainly get a stay on any punishment the NFL tried to give until the lawsuit (which I agree would never end) was settled. At the end of the day, it's his team, and the NFL will have a very hard time telling him he can't do what he wants with it without being targeted by an antitrust suit.
Only way it wouldn't result in a lawsuit is if the NFL issued some sort of slap on the wrist punishment that Kroenke didn't see as worth the bother to fight.
All this said, as long as Kroenke continues to jump through the hoops to make this whole process look good, I'm all but certain the owners will go along with him, as it could be any of them in that scenario in the future. As Hartmann said, the argument that the Rams had a lease, went through arbitration, then presented a plan to bring the EJD into compliance, prevailed and St. Louis declined is going to go far (IMO) to satisfy the requirement of trying in good faith to stay.