Janeway and others, particularly in the early episodes didn't give the Doctor favourable treatment compared to flesh and blood crew. He was a program confined to the Medical Bay. He was often left 'on' and complained no one cared enough to shut him down. What about when he was shrinking? It was like we'll get to you when we can. Because he was a hologram he was treated less than human until he became humanised. Yet he was always going to be just a hologram by 'nature', so Janeway's (later) special treatment was not going to be tailored to how she would discipline a Federation crew member, or an ex-Marquis, or a Borg. Janeway treated Neelix and Kes differently as well. The command structure of Voyager took in those who were not strictly part of it. I would suggest the Doctor was but not as a recognised Officer with pips on his collar but as an Officer in title only and as an emergency program.
When Seven threw Species 8472 under the bus in Prey she was disciplined.. barely. Janeway very next episode had to acknowledge that traditional forms of discipline couldn't be applied to Seven resulting in Seven and the Doctor (Retrospect) causing the death of another, Kovin. Borgs make mistakes, holograms do too. However I get that Janeway couldn't apply the same methods of discipline to either of these unique members of her crew. The Doctor volunteered to have his program returned to its original state in Retrospect. Janeway decided that wasn't appropriate. She was right. Just for the sake of following a protocol the loss of the Doctor's improved usefulness would have been a long term detriment. Same goes for his Command abilities. Why take away an emergency fail safe? As it so happened he could be trusted with (Emergency) Command.
Janeway treated the Doctor differently thoughout but he was different. At times I think she was very pragmatic. She DID care for the valiant hologram she befriend, but she knew how to manage her resources, human and otherwise.
The Doctor’s problem in the early episodes is that he was created overly sensitive. As a doctor, he should have understood “triage”, choosing priorities. Crew members were pretty busy early on putting out crises much of the time and his problems were low on the scale of emergencies. As an Emergency Medical Hologram he should have understood that. And yes, early on he wanted to be turned off. Then later he was annoyed when he WAS turned off. Zimmerman programmed the Mark I to be self-centered and irritable, like himself, which was dumb on his part but amusing for the show. However, the EMH was always intended to be a tool to supplement a starship’s medical staff in times of emergency. Nothing more. Do I offend my laptop when I leave it running or shut it down--? Should I care?
Capt Janeway did chew out Neelix royally when his friend talked him into stealing medicine from Sickbay to sell to get a map in “Fair Trade”. He was threatened with being asked to leave if he did something like that again, as I recall. And Seven was not “barely” disciplined. Are we watching the same show? Seven’s access to the ship and its systems was severely restricted after “Prey”, and in a following episode Chakotay told her she would have to earn back the captain’s trust. Janeway had to talk and work with Seven quite a bit over time before she came around; some of that was by appealing to their shared humanity, sometimes it was by asserting authority over her. Both was needed.
Kes was never disciplined because she never disobeyed orders or betrayed the ship, as I recall. Not until that later goofy episode “Fury”, when she had become mentally ill or something, and then she went back to Ocampa anyway.
Actually, at the end of “Retrospect”, the Doctor did delete the information he’d added about psychology, since even he realized he did not have the wisdom to apply it appropriately or to use the proper caution. He had gotten someone unjustly killed! At the very least, Janeway should have made it physically impossible for him to add to or change his programming without the captain’s authorization, since so many times his tinkering went awry.
And no, the Doctor demonstrated he could NOT be trusted independently with Voyager’s command codes. “Renaissance Man” was the next to the last episode. The Doctor disobeyed the captain’s direct order; he attacked several senior officers and impersonated them as well as the captain, then used the command codes to eject the warp core. If the crew had not found where it had gone in time, Voyager's crew could have been stranded in that part of the Delta Quadrant for the rest of their lives. I’m not saying the Doctor can’t be useful or should never be allowed to act as ECH, but only under human authorization.
For someone such as myself who grew up watching Capt Kirk liberate numerous societies that had become enslaved by powerful, computerized Artificial Intelligences, or androids, the doctor’s journey and demand for “rights” is not a stand in for real life oppressed peoples, but is frustrating and alarming. In the beginning of “Renaissance Man”, the Doctor declares that he is no longer aspiring to be human because he has realized that he is superior to humans. And then to see what he proceeds to do to his shipmates is not cute or clever. It is creepy. Computer programs and holograms are made for man, not man for computer programs and holograms. They need to be properly restricted to their defined task or turned off/deleted; and yes, in this case they need the doctor’s medical skills, so he needs to be strictly managed.
I agree with Prax. Plus, I have never much liked or fully “suspended disbelief” of the holodeck/hologram tech. And I question the cost effectiveness or practicality of using the other obsolete Mark I EMHs in mines (but that’s another topic). It is arrogant hubris that leads people to create human-like replicas, and then sentimental fantasy to believe there is no difference, or lastly, to think that because it is different that you let it run amuck. Perhaps the next Star Trek incarnation should be “The Rise of Landru”.
