Sure, permissions are the problem, but permissions are also necessary to give the agent power, which is why users grant them in the first place.

There is inherent tension between providing sufficient permissions for the agent to be more useful/powerful, and restricting permissions in the name of safety so it doesn't go off the rails. I don't see any real solution to that, other than restricting users from granting permissions, which then makes the agents (and importantly, the companies behind them), less useful (and therefore less profitable).