Ships would not be more likely to mutiny than divisions or regiments, and you're not going to lay off of building those, are you?
Some nations will be huge in navies. Imagine you're playing France and you beat Britain in yet another long war. You overran all of Africa, crushed their invasion forces on the continent, and only their navy remains in the fight. They have not conceded defeat yet. Imagine the feeling when now you see the Royal Navy in the Channel hoist the red and black banner of revolt, and turn into port in Southhampton in mutiny... and you know, *now* your time has come, now His Majesty's government will give you anything for peace!

That should be a rewarding moment, the moment when you have broken your enemy! The idea is that important things which could happen in real history, should be able to happen in Victoria 2 too, outside of a straightjacketed true-to-history event system.
With the changes that King mentioned in the rebel system, there will always be a risk that one single revolt by a POP or a regiment sparks off a huge uprising. But for that to happen, the country needs to be in very high militancy and the rebel movements need to be organized already. Else you just get a revolt that fizzles. The random naval mutiny by some destroyer in Africa would be just that sort of thing... a little fizzle that you hardly notice. The ship would be back under discipline before you can say "HMS Bounty".
It would just be in those troublesome times when your country is seething with rebellion, after a counter-revolution or a lost war or a huge political event, that you would need to fear your soldiers turning their rifles and guns on you. But that would hardly be a change, and should be a welcome addition to the gameplay.
This seems like expansion material to me. I have a feeling getting rebells to use ships is going to take some work.
I do like the idea though (and agree that it could be made intuitive by linking ships to soldier pops in the provinces they are commissioned).
I am thinking so, too. But the game is only due late in 2010, maybe they might still consider it.