Leading off with the fact that it's totally reasonable to fit a desktop on or under a desk. If you have the desk room (there are different kinds of desks), a tiny one can fit on top, there's a guy on my floor that does that right now. If you have anything larger and up to a midtower, it can fit right underneath the desk and next to the chair with barely an inch to spare.
Also, here's some advice based on experience, and the second reason for why I'm using an alt account for this (the first is that I don't want WPI associated with my main account). Go with the cheap laptop + good desktop approach, there is no laptop that can take years of schoolwork. I've got something of a motor disability, so I've been carrying a laptop around with me for 6+ years. They don't last long unless you're really, really careful. They get dented. The hinges die. They lose rubber feet, plastic panels, screws, pixels, you name it. Do you really want to be carrying around your most expensive device and your whole world in one so-easily damageable device?
Get yourself a decent desktop and a respectable but low end laptop. If you're creative with your tech, anything will do (for reference, I've got a 7 year old Gateway with a 1st generation i3 in it). Get a good file syncing solution and keep your stuff on the desktop, that laptop should be at best a proxy for your desktop. Drop some money on a foam cushioned case for your laptop - good ones are in the $70 range, but it's worth it if it makes your $600 laptop last 4 years. If you break your laptop... maybe send me a PM, I repair tech for free.
Besides, if you plug a desktop into an ethernet connection, you get a gigabit-speed connection... to me, that alone makes it worth it.