I agree with what your saying, that there comes a time when you forget about the rules and just make music, and it is a pure sense of nirvanna once you reach this platue. But I see 2 flawls in what you are saying;

1) How can you learn to hear something that you don't know exists? One must 1st learn about the scale and it's make up before they can start to hear it. I think this especially true with man-made scales such as diminished and whole tone. The major scale emulates the sound of nature, so our ears are used to hearing this, but other exotic scales have to be heard before are ear can start to write melodically w/them. So it comes to the point what came 1st the chicken are the egg (science/emotion)

2) I feel it is a major misconception that learning theory will inhibit your creativity, you can't break the rules if you don't know what they are. I think the ear naturally hears the diminished chord resolving by half step, so one must teach oneself not to resolve this chord by half step and "learn" the sound this will emulate. I think if you don't learn theory chances are your jazz songs will sound a lot like everybody else's vrs. if you do.