It may not be in my best interest to ask a professor I have done research with for recommendation letters. Can this seem suspicious in my application?
the professor has told me several times he would be very interested in having me as a PhD student. So, I guess, he may not appreciate the fact that I have decided to pursue another area with another supervisor

Could be, if this person is vindictive and unethical. But if they are a decent human being they would write a gushing letter about how they would love to have you as a student, and other professors would take this as a good sign.
Unless you have a stronger reason to think this person falls into that bad category, I think they are probably one of your best potential letter writers. Someone who wants you as a PhD student is someone who has confidence in your research potential - that's exactly what you want from your letter writers.