Right, but it seems like during it's OTL run Voyager went out of it's way to avoid any risks and just be TNG 2.0. It would be interesting, yes, but it would require some secondary PODs as well.
They could flow organically from the original POD.
We start with Bujold taking off after a few episodes are in the can, as stated. Paramount isn't going to just stop production on the program they've spent so much time and energy developing, so it's decided that things will continue. A script is quickly developed to fill the gap: Captain Janeway dies on an away mission, sacrificing herself for a noble cause, obviously saving her crew in the process. Chakotay fills the captain's chair. While uncertain about the situation, Tuvok initially accepts him as the new Captain out of a respect for the chain of command.
Back in the real world, though, actor Tim Russ is somewhat uncertain over this development, and asks the producers if things would really go so smoothly. He specifically points at Deep Space 9 as an example of positive storytelling stemming from outright friction between the characters. Robert Beltran agrees with him. Not wishing to cause any further problems on a set already thrown into chaos by the departure of their lead actress, the producers promise them a story arc that will address these issues.
Back in the Voyager universe, friction begins to develop even further between the former Maquis members and their shipmates, as many of those who stayed with Starfleet are chafing under the idea of serving under a Captain who turned his back on The UFP. While Tuvok initially attempts to hold the line, he is slowly swayed by the logic of the arguments of his crew. However, he is a Vulcan who plays by the rules, and he continues to support the Captain for the rest of the first season...until the season finale.
At the end of the first season, Voyager runs across a communications array that enables them to contact Starfleet in something approaching "real time". The technology itself is far in advance of current Federation capabilities. All that the crew knows for sure is that they're only going to be able to use it a few times to send important messages back "home", and perhaps receive a message or two in response.
There is indeed one message from Starfleet that comes on the viewscreen: Captain Janeway's pardon of the Maquis members of the ship was totally unauthorized. As she is no longer in a position to defend her actions due to her noble sacrifice, a decision has been made at the highest levels: "Captain" Chakotay's field promotion has been rescinded. He and all other former members of the Maquis are to consider themselves on a temporary probation until the ship reaches Earth, but they are not to be placed in any positions of authority.
As the tension between the Maquis and Starfleet aboard Voyager reaches a fever pitch, Tuvok calmly informs Chakotay that he, Tuvok, is now taking charge of the ship per Starfleet orders. B'elanna Torres, now on the bridge, pulls her weapon and aims it at Tuvok.....
"To Be Continued...."
BUM BUM BUM! BUM BUM BUM!