If you're going to efffectively deal with this teacher and continue using Perl, you're going to have to do additional work. Handing in a Matlab version of one or two assigments, along with Perl versions, is a good start. You also need to annotate the code, explaining where you've made different choices for what you're doing, and why, according to the possibilities inherent in the tools. If you can do this in a firm yet respectful manner, you may be able to win him over.
You also need to make sure you aren't getting around the guts of the assignment by using special features of Perl. If you're asked to implement pattern matching and you do it by using Perl regexes, you probably deserve to be failed, since the assigment is to implement, not to use someone else's implementation.
They laughed at Joan of Arc, but she went right ahead and built it. --Gracie Allen