If they were allowed to stay in Starfleet when they got back to the AQ, I would have liked to have seen Tom and B'Elanna working in ship design.
In my last comment, I wrote that I thought that Tom (and by association, B'Elena Torres) stood a better chance than Chakotay, Allaya, etc.. in the view of Starflett command staff, well, I refered on his great chance to escape prison thanks to his proeminent supporters BUT don't dream, Tom - as B'Elena - would NEVER be reappointed by Starfleet and certainly not with permanent ranks for the simple fact that technically, it would be difficult. Indeed,
Tom was
dishonorably discharged from Starfleet (the man redeemed himself a conduct but NOT the ranked officer he was) and
B'Elena was maybe one of the finest students that professors had ever taught but
she dropped out even before she graduates (in fact, if we take into account her short past at the Starfleet Academy, she was still a cadet when she left Starfleet to join the Maquis, right?! So, she would have to reapply to the Starfleet Academy, to graduate out in the first ... and to count on the support of her stepfather, Adm. Owen Paris & Janeway, newly promoted Adm, to get precociously, a commission as Lt Jr or even full Lt in order to work in their engineer dpt (*)!)
Plus, according to what I saw in the 172 episodes, although Torres was a lovely person, able to be friendly and fiercely loyal, she wasn't less emotional there (hot-tempered when things do not take place as she would want and in the speed she desired, struggling to follow protocol, still not ready to make concessions in her principles...
In short, B'Elena is a brilliant individual but wouldn't fit in a military organization like Starfleet and we could say the same of Tom!.
However, the Paris couple could be hired by Starfleet as civil experts (Tom in ship
design & B'Elena in engineering). So, enjoying financial, material and technological benefits offered by Starfleet but far from the protocol, from the politically correct, etc... .