I think the crew and Janeway would have faced the mother of all debriefing sessions when they got back, even more so since if they had transmitted all their files before they returned there would have been even more questions to answer. I wonder if by then dead issues (such as the Maquis) would have been bothered with, but what about the Equinox business, or the episode where they awoke the two warring races and then just left them to their war again? Surely those actions were so serious they couldn't be ignored, even if they did deal the Borg a heavy blow. What about her abuse of the time travel to get her own way? Do you think she would have put in her log that she came back from the future to significantly alter a timeline she didn't like or would Temporal Agents have detected it anyway?
She would have certainly fought for Seven, but Seven was so de-borged by the time they got back they would learn more just by asking her about her technology, and reviewing the ships logs.
Still can't figure how she got Admiral though!