Would you like to share that workaround?
I do understand why Unity changed the way the objects are deactivated, but, having used the previous way, it's more than annoying to have to do a lot of things to have a single object in a lower level of the hierarchy activated.
But, for the scenario you mention, is like you have the object outside of your panel (let's say, like a pickup in your world?), then, if you pick up it, it'll send an event to a manager, I think, so it'll be added to your panel. So, if my assumption is correct, your panel does not need an FSM, and it's not a problem if you have all its hierarchy disabled in a given moment. Just have your manager listening to those events your items send. Perhaps you have this issue because you initialize your pickups being parented with the panel, but somehow, you only relate them after being picked up?
Remember that Playmaker does not implement what it does, but it calls Unity functions. So, if you want Playmaker to be no longer recursive in toggling GameObjects, you might have to check if Unity has a way to do so from Unity 4.