As a programmer, I would suggest getting a full laptop for somebody majoring in CS. As much as I love the transformer, you cannot compile code on it. At least in my searching I have not found a single IDE meant to be run on Android (Lot's target Android, but none run on Android). More than likely, there will be several times that you want to do work away from your room. On the transformer, the only real way to do this will be remote desktop software. It's up to you whether you think the remote desktop software will be sufficient for this, but one other thing I would caution against is the small keyboard. It is far more comfortable (and efficient) to program on a full-size (or as near to full-size as possible) keyboard.
I don't know what type of program you are going into, but if you take any courses on 3d graphics you are almost certainly going to lose the ability to test your programs through a remote desktop connection.
I personally think that tablets are great in conjunction with a desktop. I plan to get rid of my netbook once I get the transformer. My only concern for you is that a tablet simply isn't a good tool for programming. If the hacker community manages to get ubuntu onto the transformer then the device will be an acceptable programming tool in my opinion; although, you will still lack a full size keyboard.
My advice to you is wait until mid-to-late summer. There is a slew of new tech toys coming out this summer, and almost anything you get now will be outdated by the time you start in the fall. By summer you will know if we managed to get Ubuntu on the transformer, AMD's Llano processor will be out on laptops, and Tegra 3 tablets may be just around the corner.