Usually they are pretty steadfast. Unless they see that you took an extended humanities series. Most schools say that they will accept AP credits only in the place of Science courses, with the expectation that you will be taking more advanced courses in the areas that you tested out of. Some medical schools do not accept AP credit for any of the required prerequisites; an example of this is most of the UC schools.
As for your situation. I wouldn't worry about explaining it in your primary application, but when the individual schools start sending you secondaries, make sure to mention that you have accomplished some sort of writing composition in some of your other classes. It's funny how I too was pushed to take AP courses while in high school, yet I ended up having to retake the courses in college anyways to meet the requirements of the UC schools.
A safe bet is to call the schools your interested in, and explain your situation. I'm sure you'll have a sympathetic ear that will listen to your dillemma [sp?].
Good luck in the application process. 🙂