Were the Maquis who returned on Voyager punished for having been Maquis?

Question

In the first episode of Voyager, Captain Janeway permits the survivors of a Maquis ship to join her crew, even though from a legal perspective they are outlaws at best and terrorists at worst. Later on, the Maquis as an organization

is annihilated by the Dominion.

What is the general fate of the former Maquis members who survived the entire voyage, returning to the Alpha Quadrant on Voyager?

• Are they allowed to continue in service to Starfleet?
• Are they pardoned for any crimes they had committed while in the service of the Maquis as a "thanks" for serving on Voyager but sent on their way (e.g. no more serving on Starfleet vessels, but no particular punishment either)?
• Are they delivered to the Federation criminal justice system to stand trial and/or face punishment for their Maquis participation?

If the former Maquis receive individualized evaluations and determinations, for example, a select few who had served with distinction have their ranks confirmed/ratified/made permanent by Starfleet Command, most of the rest are kicked out onto the streets of San Francisco, and a handful who had committed particularly egregious crimes before their Delta Quadrant detour are given prison sentences, that's an answer.

Answer 1

Ronald D. Moore felt that had the show continued beyond the ship returning to Earth, the money-men would have insisted on the crew remaining integrated and that the only serious way that could happen is if the Maquis crewmembers became fully-fledged Starfleet personnel. He hated the idea and resisted it heavily.

I said this years ago: it’s giving up on the show. If you bring that ship home before the series is over, you have given up. You’ve rolled over and said, ‘We can’t make it work. Let’s just go back and do TNG all over again.’ It comes back home, goes to Earth, there’s like a two-part episode as they go down to Earth and revisit their old lives. What’s going to happen at the end of that two-parter? All the characters are going to re-up and say, ‘I love Voyager. It was such a family. I learned so much from you. Let’s not break up. Let’s stay here.’ All the Maquis people will take regular commissions in Starfleet. Chakotay will chose to be second in command to Janeway. B’Elanna will embrace those warp engines.

_{^{Ron D. Moore - Q&A - LCARS}}

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In the EU continuation novel Homecoming we learn that with little left to rebel against (and with the dire need for good officers to man ships against the Dominion) the Maquis were issued a general amnesty and pardons for those in jail. The crew of the Voyager were extended the same courtesy on their return.

“During the last days of the war there was a shortage of trained, capable officers. The situation was desperate. A general pardon was therefore offered to any of the Maquis who chose to return to Starfleet, absolving them of any wrongdoing, and after the massacre on Tevlik’s moon, it was argued that there was no reason to doubt their commitment to the cause. To be honest, I opposed the amnesty. I did not think Maquis could be trusted. I have never been so happy to be proven wrong. The former Maquis served bravely and loyally. Therefore, I hereby extend the amnesty to all those who Captain Janeway informs me have served her so well.”

Admiral Paris smiled, then spoke again. “Which means I’m spared the unpleasant duty of escorting my new daughter-in-law to prison.”