No he can't buy MS Office through the MAS, but he can buy iWork, which worked just fine for me in all of the papers I had to write in college. That makes the difference $500 - $880 vs $900. (The base 13" is $1200, $1100 after edu discount, then take out $100 for the app store gift card and $100 for the printer). Now obviously this would depend on if he is getting the PC at the lower or upper end of that price, and if he can make do with iWork instead of MS Office (perhaps we will see Office in the MAS in the future too??)
No doubt PC's are cheaper, but if you can use promos and discounts to your advantage, you may be able to make the difference in price more minuscule.
And as far as the printer goes, you can get any printer at the apple store or on their website, and if it costs over $100, you are just stuck paying the differences. Here is a page on apples site with some of their printers offered in this rebate...
http://store.apple.com/us/browse/home/campaigns/printer_promo
And as far as ink goes, most students are not printing out pictures or full color pages, just typically essays and papers that need to be turned in so you really only use a lot of black ink.