I am in CS. Your right that it won't hit your computer too hard in undergrad. If you do get hard hitting stuff (i.e. parallel programming) you are likely using university provided computers instead.
I wouldn't spend to get the upgraded 13". However, the main reasons why I got the 15" are:
(1) SCREEN REAL ESTATE! Having two 80-character width files open side by side is a godsend when coding. If you use emacs you can get away with 2 files open side by side at 1280x800, but just BARELY. 1440x900 is really what you want for 2 files comfortably side by side with some wiggle room left over. If you always have an external monitor handy this isn't an issue. However if you are in a classroom, out in a coffee shop, working with group mates somewhere, travelling, or even just in your bed working, you won't always have an external monitor. If you get 15" you might as well get the hi-res upgrade to 1680x1050. With that resolution I can open 2 files next to each other with plenty of room to spare.
(2) I do parallel programming, having more threads helps me catch some race conditions. Also I tend to have TONS of stuff happening on my computer at once and I compile some very large programs. 4 hardware threads is better than 2 in this case if you can parallel build your programs (the -j flag in make).
Screen real estate is the real kicker here. If I need to I can always SSH into another machine (with hundreds to thousands of cores) to do my parallel debugging, but I can't get the screen real estate when I'm anywhere else but my desk (which has 3 monitors and 2 more computers btw). I travel at least once a month so I need screen real estate on the go. As a student I suspect you may want it also.
Summary: I would recommend the base 2.4Ghz i5 model with the hi-res upgrade. Glossy or Anti-glare screen is up to you. Also an SSD does wonders for compile times, if you can sacrifice the extra space and shell out the $$$ for one. Look at my sig for what I ordered. Note that compile times for anything you do in undergrad shouldn't be more than a minute anyway though...unless you like to use some funky languages...