Unless your course requires the laptop to communicate with some very low level hardware such as eprom programmers, or requires some built in encryption hardware, I don't see a problem using a MacBook. In the first case, I would only see a problem if the laptop would require a serial or parallel port. Although the MacBook probably hasn't be 'proven' with such devices yet running MS Windows.
I suppose they could be picky about MacBooks only having beta support for MS Windows. Again, they may consider this 'unproven'.
Lastly, will you be writing or running code that talks to the hardware in some manner. This could be an issue if the machine they suggest have it and the MB does not.
If all your going to do is run or write software that does not require any of the above, you should not have any issues. The school should provide solid reasons for their requirements or shut up.
If you end up having to buy one of their two options, buy from another source other than them. Educational discounts are often available from other sources. I wouldn't want to give them a profit.