This is a great question that I think a lot of students have. Let's take this question point by point.
First, does music theory knowledge impede one's ability to improvise? Actually, I think it is actually the opposite. When we study music theory we are learning the ways in which music can be expected to behave in certain situations. Of course harmonies have functioned differently in different eras of music, and continue to do so today in different genres. For example, Mozart's conception of harmony and tonality was different from that of J.S. Bach. Musical thought evolves, music changes, and composers begin to experiment with new ways of moving between harmonies, or new formal structures, and so on. Music theory ponders ways in which music can and does function, and knowing how to properly conceive of and execute a musical idea requires at least a certain degree of knowledge. The idea that improvising something is to act with no forethought is a common misconception. Just as when one is in a verbal conversation their responses may not be pre-planned, but they do still follow basic rules of grammar, syntax, and style. One would be expected to respond to another in the same language, about the same topic within the same context rather than just saying a string of random sounds.
As for having a doctorate in music theory putting you at a disadvantage for a position as a conductor, this again is a falsehood. Conductors must be adept at music analysis in some very deep and meaningful ways in order to be an effective ensemble director. Conductors spend months, and even years, analyzing a work before even approaching a rehearsal. Furthermore, conductors must make their analyses come to life. What one is hearing when they attend a concert is the conductor's interpretation of the score. They are bringing to life how their analysis leads them to an interpretation of the score that they are presenting to the audience. Conductors perform an analysis as a way of saying "this is how I believe the piece should function/sound."
Finally, is there anything about learning music theory that slows down your musical capabilities? My answer is a firm and unequivocal 'no.' Strong music theory skills will make one a better performer, conductor, improvisor, and musician in general.
We must always remember that music theory is not a set of strict rules, but rather a set of historical examples that show us how music usually functions in certain specific situations. It is our job as musicians and theorists to continue developing ideas about other ways in which music can function.