First off, it's completely normal for ball pythons to hide often, that's just how they are.

For handling or cage maintenance and such, it is completely fine to just lift the hide off the snake and take him out. It won't make him aggressive in any way, so long as when you put him back in, you put the hides back in as well. Otherwise if you were to wait until he is out to handle him, as you saw, you may hardly ever get to handle him! don't worry about lifting the hide off of him. That's how I do it with all my snakes (and pretty well everyone that has ball pythons does it lol), never had a problem with aggression