That's the dilemma.Yes but just because you have shown that you are sentient and possible a new life form doesn't mean you should not be punished or fixed to prevent you from doing it again. After all if he was a human doctor, he would be seriously punished, possibly even court martialed.
All the more reason he should have been punished, imo. Sentience implies free will and someone with free will can be held accountable for their decisions and actions - new life form or not.
Now if the Doctor did not have sentience/free will you could just reprogram him to not do it again. Problem solved. Since that is not an option then he must face the consequences of his actions.
The Doctor isn't a "someone" but yet a little more than just a computer program now.
Wouldn't we have to determine exactly what he is first?
It's the arguement of Issimov's "I. Robot".
If you create a thing and allow it to grow, then you better be aware of what you're creating and set laws of governing it accordingly. As of yet, there are no laws governing the EMH because they aren't sure what he is yet.