I would be thinking about starting at some place far easier than MD5. A book on the history of cryptography could be helpful. It been a decade since I read a book like that and my memory is fuzzy.

Anyway, I would be thinking of starting with simple substitution cyphers, like ROT13 and variants. Some basic probability math would be appropriate with this subject.

I could envision a number of fairly simple programs to help break a code like that which could be done within the time frame that you have.

I forget the names of many early ciphers, but these things that used various lookup tables, etc. are implementable with basic programming. If you have to get into low level details like binary polynomials, then the basics of what that is and how to program that could overwhelm the students. There is a limit to what you can do in your 1/2 of the 2 weeks.

How say DES works, could be a lecture, but I doubt a student could go from "ground zero" to working code in 2 weeks, even with the algorithm clearly spelled out.

Update: you could have some fun with the Unix password encryption system.