Well...this is an interesting question. You can get by and probably enjoy movies in stereo...especially if they'll be played through nice speakers like Axiom towers. It's really a matter of how loud you can turn it up before your neighbors hear. I don't thing you'd have any problems running surrounds and have to worry about neighbors, unless your surrounds are on a wall connecting to their wall...but then still it's a matter of how loud you play it and how well insulated the walls are.
The subwoofer is a different story all together. Generally most of your speakers can get to a decent volume and not disturb anyone, but a sub has signals that can pass through walls pretty easy if they're loud and low enough...especially if there's neighbors below you. This would be one you'd have to keep at a low volume, or do what I'd do...try a different level each night and see if you get any feedback from your neighbors
If you're friendly with them all the better. Let them know you got a kicking new system and you want to test it out and see how loud you can play it without making any disturbance. They'll thank you and respect you for this approach. Heck...invite em over for a show and you won't have any worries about the volume then.
So, in my opinion both are okay, but if you can swing it go for the 5.1. It's just a more immersive experience. And if you're like me, an avid gamer, most games (especially XBOX) are being designed to be in surround sound so you know where stuff is coming from. Something you just can't pull of in stereo. My feeling is you'll be fine with 5.1, just keep the volume respectable. And someday when you have your own place (house/condo/whatever) you'll be thankful you already have your setup complete.
This is all of course my opinion. But I'm partial to my advice
Good luck!