I honestly think it was meant as an inside joke and big "F-U" to Mulgrew for not allowing Janeway to have an on going romantic interest like they wanted. I think they wanted to get Janeway & Chakotay together for a long, long time and Mulgrew heatedly refused every time. The writers knew J/C was part of the dynamtic that could have improved the show and brought in more viewers. So their answer was to Mulgrew was, then Janeway will never have him and paired him up with Seven instead. So because Mulgrew wanted Janeway to be all career, a career is now all she has.
Plus it being the last ep., Mulgrew couldn't debate it.