This is definitely a good idea, but I can see it being abused... Red team notices that Blue team is stacked, so in game, they just sit there and do nothing while the stacked team kills them... 0 score forces a ship switch...
If the loosing team can't coordinate themselves to fight effectively how will they coordinate a mass lay down and die protests?
I think the potential for abuse comes more from the stacked side which can feed the other team a pity kill to keep their team together.
Also if the teams are stacked because one ship is really good, there is only a 50% chance a ship shuffle will result in a loosing ship ending up teamed with it at the end of the shuffle.
That's the only concern I have with your current suggestion... I think that the ability to switch sides for the entire crew could be extremely useful, so I'm not saying to through it completely out... just the idea of when to use it
I envision it working by at the end of the match the game checks the score for 0 on one team. If it is 0 all member of that team get a poppup message saying:
"That went rather badly, would you like to shuffle the ships?"
Only when more than 1/2 the loosing team votes yes does the shuffle occur. That way if the loss was a fluke in an otherwise even game the loosing side can elect to stay together.
Muse of course can implement it however they like, if they choose to implement it at all.