Would have to say, it would be best to force all smaller ships to travel via Jump Gates. Only large ships could fit a Jump Drive.
However, I don't think Jump drives should take the large ship alone with it. What if the Jump Portal Generator created a jump field 1km wide (as an example) that pulled anything in it along with the large ship with it. (Accept other Large ships to prevent them getting cut in half)
BTW: JPG = Jump Portal Generator
Interesting note, if you ship is longer then 1km then you would need to add additional JPG's in order for it to be able to jump. (Which by the way I think would make an excellent balance mechanic for large groups of players making something that big, due to the insane cost of say activating 5 JPG's)
Further-more, a Large ship shouldn't be able to jump somewhere the Navigator does not have the coordinates to. (IE Someone has to have been there, and gave the coordinates to the navigator if he himself had not been there)
Finally, there should be a limit on how many JPGs can be used to go to one place at any given time. (Stops 200 Large ships from all jumping at the same time and landing at the same time, causing the greatest intergalactic car crash you have ever seen)
(Also i'm totally gushing this one but)
Would be awesome if you could activate a JPG over a city and take the top half of a city building with you.
Because, that is my favorite moment from Halo 2
(But would also be used to grief to no end)