"I've noticed that a few genres of music tend to discourage it"
Which genres? Be specific. Jazz is the most improvisational genre I know of and they strongly encourage learning theory.
"I just read that learning music theory "seems like the antithesis" of being able to improvise."
This is very sad. Nothing could be further from the truth. I will delve into this later.
"Apparently, having the equivalent of a doctorate in music can actually be a disadvantage if you want to get hired as a conductor, because they think you're too theoretical."
I've never heard this before. Again, can you cite a reference of give examples that you know of where a PhD musician applied for a conductor's job and was turned down for this reason? Or is this just a perception?
"Is there anything about learning music theory well that slows down your musical capabilities?"
No! Other than a general misunderstanding and fear of learning.
Now I shall try to delve deeper into this phenomenon, drawing on personal experiences.
I think that people misunderstand what music theory is and how it is related to our use of it as a tool for creating art. The same could be said of painting, sculpting, etc. Does learning theoretical treatments of light, shape, geometry, perspective, etc, suddenly make you a poor painter? Never, I have literally never heard of this happening and most artists jump at the opportunity to learn more about how to manipulate 2-dim to create 3-dim. Of course the artist can choose to ignore this and work in abstracts, etc. But the really good ones understand that to hook the viewer they need to express the "thing" being abstracted. One can VIOLATE the rules of shading to create visual illusions that will mesmerize the viewer. But you need to know the rules and how they are perceived to know how to break them.
Here is where a misunderstanding occurs. It seems to me that when learning music theory, specifically Western Music theory including multi voice Harmony, we learn that certain combinations of tones etc "work well together" and immediately we assume that anything NOT described by these rules has no chance of working well together. This is a common thing people do, if category A has a property then its complement must NEVER have that property or have the opposite properties. Unfortunately this is not generally true, especially in music.
As an art form we are free to put tones together or in succession "in time" or out of time as we like. For whatever reason, reasons that I personally do not understand and doubt that there is any real theory behind, some combinations are "generally pleasing to the listener" and others not. What western music theory explains is this general trend that is widely accepted not only by musicians but, via trial and error, by the uninitiated audience. In some sense you could consider what you learn in music theory as a set of "best practices" guaranteed to almost always produce "music" that is not offensive to the ear. Whether or not it becomes a "hit" requires more than just following a rule set.
There seems to be a tendency to interpret western music theory as being sacred or almost grounded in physical law, like physics. You can't violate the laws of physics but you can violate the "laws" of music theory. I think people give too much credit to this body of information than it deserves, or they misinterpret what it represents. As I said, it reflects best practices in the western musical tradition and not a universal set of unbreakable rules or laws.
Does learning this make one less musical? Sometimes it can. Again, this comes from how the information is presented. Here is a personal anecdote. I learned music formally, classically, at a very young age. I grew up around working Jazz musicians too. I started going with some of them on "low key" gigs just for fun in 7th or 8th grade (age 12 or 13). I played everything by ear, noodling around. I got a lot of complements after a while and the other players were very supportive, saying that I had "good ears". I don't think they were fibbing, they're pretty honest and would tell me straight away if something was off. Then comes my music theory lessons. I learned theory in school and in private guitar lessons at about the same time. As soon as I saw a set of rules that said "Do This" I immediately thought "Oh crap, the thing I do are not in the rules, better stop that." Biggest mistake of my young life. I eventually got over that and went back to playing by ear but from this experience I saw the misunderstanding that was causing a lot of my friends to stay away for theory like the plague.
The truth is you can't "think" of anything when improvising, not even how to play your instrument. This will screw you over every time. So on some sense everything we learn has to be ignored. But this doesn't mean that leaning is fruitless. What we invest in learning theory and practicing gets imprinted in our subconscious mind and works behind the scenes when we improv. In my opinion you can NEVER get worse by learning more. You need to put it all in context.