I faced a similar situation. I was considering a formal diagnosis at the same time I applied for a law enforcement position. When I learned that part of the process would be a lie detector test, I decided not to pursue a diagnosis, since while it was unlikely they'd ask "Do you think you have a mental disorder?", they may very well have asked something like "have you been formally diagnosed as having any any form of mental condition, such as depression, bipolar disorder, etc..." At least without the formal diagnosis, I can answer yes truthfully. I ended up not getting the job for unrelated reasons.
Wikan, you just have to ask yourself, honestly as possible, if you feel you can do the job of a physician even with your Aspergers. If you feel you can, that it won't get in the way, then I'd say you're doing the right thing.
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Everything would be better if you were in charge.