Janeway couldn't punish him because they allowed him for 7 years to become what he is at the end of the ep., which is possably sentient. Janeway would also be punishing him for the right we all have, the right to make a choice.
Tom made a choice to help out some aliens in
Thirty Days against Janeway's orders, but he got busted back to ensign and sent to the brig for a month. By letting Dr Shmully off the hook she is confirming that he is different and that he's not to be held to the same standard as the human and human-shaped aliens in her crew. She was not treating him as an equal, she was treating him as a child.
But that was never my point, my point was that I never believed that the characters would act this way. In order to get the plot where the writers wanted it to go they had to make both Janeway and Shmully act out of character and I didn't buy into it. I admire what they were trying to do but plot determined character actions, it is supposed to be the other way around.