we made plenty of modifications to my dormroom, and subsequent apartments, without being charged. haven't you ever heard of toothpaste? you don't necessarily need to bolt to the floor if you want something light, just find some studs in the wall. drywall is easy to patch. unless your RA/RD is an incredible jerk - which you have the power to overcome by being sociable - or unless you are a really foul handyman - again, totally up to you - there shouldn't be a problem. at least no problem greater than hanging posters with duct tape instead of sticky tacks, which everyone does. little putty, little paint, good to go. try rebuilding a wall after 8 months of a dartboard with no backing, then it starts to get more frustrating. remember, you can move furniture around too. if you do want to drill the floor, do it close to the beds, fill with some compound, and just shift things slightly on your way out. i see nothing wrong with that because as long as you patch, there is only minimal aesthetic damage, which you've covered with something, so it's pretty much a nonexistant harm. weigh that against your inalienable rights, i'd say rights win out. million ways to handle this - i am by far one of the most "creative" (read: destructive to the natural state of things) people i know and i've always gotten my security deposits back.
if you don't like that, you could always get a safe that's too cumbersome to move, or bolt something lighter into something that's too cumbersome to move (bring some cinderblocks in, or some metal piping that you build into your closet that wouldn't fit through the door without disassembly). if you're doing something heavy, though, be aware of the limitations of your building if you're on a floor a little way's up.
if none of this is appealing, you could always just store disassembled. people might cut a cable for a whole gun, probably won't just for the frame. and the nice thing is, every part of a gun is cable-able. run one through the barrel through one drawer to a desk. another through the frame in your closet maybe. one through the slide somewhere else. you're toast if the zombies are at your door, but you've made it tremendously impracticable to locate and steal the whole gun, and provided a level of security that would give you a similar amount of time to most lightweight security units.
there are lots of other ways to handle this but i need to stop procrastinating now