Is it rude not to take a course with your adviser?
Expanding my comments from earlier...

Most importantly, talk to your advisor. Either you should be able to convince him/her that the other course will benefit you more or he/she should be able to convince you that his/her course will benefit you more.

I disagree with RoboKaren's answer. Working with your advisor is far more important than taking a class with him/her for a letter of rec. You may have other opportunities to take a course with him/her anyway.