Window if down sounds like it will break when closing door

Try tightening the bolts that hold the window in place. Take off the inner door panel and roll the window down a bit, you'll see the 2 bolts that hold the glass.

While you're in there, check to make sure nothing is loose

 

Typically you use pry tools, either plastic or steel with some masking tape, and just pull out the panel. Look at the arm rests and door opening levers, there's more than likely screws that need removal, lever arm linkage and wiring connectors to be undone. The fasteners will sometimes come out properly, or they might stay in the door, or occasionally break. There's likely to be a plastic vapour shield afixed with non-hardening caulk: just peel it off as much as needed, and try to keep it neat.

Have you ever needed to break into the car, locked in a key. With a Prius probably not, but just curious.

 

Once you get in there you'll likely see what's happening. I recall a door repaint one time: they missed a bolt on the window guide, it was dangling. Not sure how that would happen with a break-in though. Maybe just something got snagged, and is now dangling/hitting.

 

Welcome, @btped! Easy peasy. I had my '05 apart several times for various reasons. This is from memory, so I may be missing a step or two but here goes:

There's a plastic thingy behind the inside door release handle. Pop that out and remove the screw behind it. There's another screw down in the well in the arm rest where you grab to close the door. Also, lift up on the control panel in the arm rest. It pops off and you can unplug it. (Two connectors on my trim level 5.)

Once you have those out, if you have the JBL speakers in the door up by the mirror, that pops off. Then just go around with a plastic pry took (or strong finger tips). I find it easiest to start at the bottom of the door toward the rear. Once you pop off the bottom, front, and back you can lift up and the gasket will lift out of the window slot. Don't go too far yet, though, because you'll need to unplug the little light in the panel down near the floor before you set aside the panel.

Then the fun part -- messing with the clear plastic and the tar that's going to be in your way.

If you want to see it done, there are various videos available on line. Have fun!
[edited for typos]