As for the Maquis, I would think that since the rest of the Maquis were pretty much all killed and the only ones surviving were standed in the DQ for years...that Starfleet would have obviously have dismissed the charges. I would venture to guess that people dedicated to their work like B'Elanna and some others would have stayed in Starfleet.
I didn't read Homecoming yet, but I have read Mosaic and the later novels by Kirsten Beyer (Full Circle --> Eternal Tide). For Chakotay, I have a little bit of trouble believing he would have taken on the job of Captain. I understand they had to have him be active simply for the plot or whatever...but if this were reality...I think he would have came home, got a position teaching Anthropology or Archaeology, and left it at that.