still I think that giving the Maquis central characters Starfleet backgrounds was a bit of a cop out
Understood and agreed, to some degree. I just don't feel quite as strongly about it. If there were no semi-Starfleeters in the mix, Janeway would probably have had a full-blown mutiny in her hands, and the ship would soon have been sailing not with 150 grudgingly cooperating people, but 47 badly maimed survivors. It would have been a different story - and probably one where the ship would never have survived past the first season, let alone reached home.
Ensign B'Elanna Torres can still give all the orders she wants as chief engineer, any lieutenants on her team still have to do as they're told because she is in charge of that department of the ship.
But it undermines her authority if her underlings hold higher rank than she does. It's as if Janeway weren't trusting her with higher rank - how, then, could the underlings trust her with anything?
Nothing would really be won by giving Torres low rank, except if the intent was to humiliate her and the other Maquis. And that didn't seem to be Janeway's approach to the issue of Maquis control.
Chakotay obviously ran a tight ship (even if it was full of spies and traitors), and would have had a rank system of some sort in effect aboard that ship. Janeway would no doubt consult Chakotay on the issue, and try and preserve that rank system, interlacing it with whatever remained of her own rank system and personnel. The other option would have been to preserve the rank system but have it categorically be "beneath" the Starfleet one - but that would mean that nobody would listen to Torres at Engineering, or Ayala at Ops, or even Chakotay at the center seat.
Well I don't think "hate crime" is really the term to be used in this situation - a murderer who has served a sentence is still a murderer and people still consider them as such, same as a convicted rapist who is eventually let out of jail is still a rapist.
The point of the law, though, is that the ex-con is now innocent of all crime. And Starfleet would have a strong interest in enforcing the point of law here.
Also, if a person isn't innocent when coming out of jail, then why should he ever come out of jail? The jail is supposed to correct him. Perhaps not in practice in today's world - but in the Trek world, that's more than a pious wish. Supposedly, all criminals are considered insane, and are put to therapy where they are cured of crime. If you get out of therapy, you no longer are a criminal (at least not on the specific type of crime that got you into that jam in the first place). You get a short bout of therapy for petty crime like Mudd's, or for treason like Paris's, or for attempted genocide like Garak's. If it doesn't work, you don't get out, but are sent to Elba II for life. For all we know, Mudd never ever attempted the use of counterfeit money or operating a starship without license again; Paris never defected to the Maquis again; and Garak never attempted genocide again...
Was Paris pardoned then? Pardoned by a captain for getting three colleagues killed then convering up the circumstances to save himself?
By Starfleet, probably, not by any specific captain (least of all Janeway). The deal for his pardon and release would have been made before the ship set out for the Badlands. Garak was pardoned/released for attempted genocide, which supposedly is much worse; Yates for helping the Maquis, which was what got Paris jailed.
For the deaths of the three colleagues, Paris apparently only got a reprimand. It was an accident, after all; probably many Starfleeters end up getting their colleagues killed, as space is a high-risk environment. For the cover-up, Paris got drummed out. But he didn't get drummed into therapy on a penal island.
She didn't owe the Maquis anything, she was good enough to take them all aboard her ship and head home, but why the need to give them positions of power?
The ship wouldn't have gotten far without a Chief Engineer. Even though Janeway couldn't predict anything specific, "Parallax" would already have killed them all had Torres not been aboard. Janeway's life depended on her enlisting the help of at least some of the Maquis - and once she did that, her life would depend on appeasing the remainder, too, lest she subject herself to a murderous mutiny.
I suppose Janeway could have made Torres a commander, but is that an appropriate rank for a chief engineer of a ship the size of Voyager?
We don't know the names and ranks of the top people Janeway lost, not as such (LtCmdr Cavit notwithstanding). But we can infer things from the casualty list that Seven of Nine reviews in "Imperfection". Cavit is not on that list, but one Commander and two Lieutenant Commanders are. We saw that the nameless Chief Medical Officer was a Lieutenant Commander, so he might be one of those two. The Commander (named J Bartlett, as per the "West Wing" theme of that casualty list) would probably not be a line officer eligible for command, or else he or she would have caused confusion by outranking Cavit. Perhaps that one was the Chief Science Officer, then? Or perhaps the Chief Engineer wasn't in the command path but was a specialist who would tend the new engines for the maiden voyage?
Since we have difficulty placing the names from that list in appropriate positions already (because of there not being sufficiently many plausible top positions), we should probably accept that the Chief Engineer used to be either Lieutenant Commander or Commander. So when Janeway made Torres a full Lieutenant after "Parallax", she was apparently holding back a bit.
She only made Chakotay a Lieutenant Commander, of course, so it would make sense to keep his most trusted underlings, such as Torres and Seska, at lower rank, to preserve the original Maquis rank structure.
Hell, Seven of Nine flies the ship on her own through a nebula.
Only for a very short period of time, though. Janeway knew she'd be facing a journey taking years if not decades. Probably not even the original Starfleet crew of 150 could have coped with that; a skeleton crew would have run into trouble immediately when the first repairs had to be made, and the full combined crew was really struggling with keeping the ship together after a couple of years. Good thing that they got outside help, from assorted friendly ports.
Timo Saloniemi