As far as part one is concerned, Mulgrew was being difficult renegotiating her contract for season 6, and they were leveraging her obstinacy claiming that John Savage would be more than happy to walk in and take over the show if she didn't bend over and take it from their lawyers.
(Oh, does that mean that Mulgrew didn't have to act in all the scenes where she's trying to kill Ransom, because she wanted to stick her foot up John's ass for trying to take her job?)
Think about how they ended season 5 with a flying space beasty going in to eat her face off.
They where creating an exit for Janeway to leave the series "seamlessly" by claiming that it's good that the Captain died now before her mania got any worse.
In the real world if they forced Mulgrew to walk, over a matter of 10 dollars, they didn't even need her presence for part two since any headless mannequin would do, to stand in for the great actress.
Hedging their bets.