maybe the govern could tell the ship to launch with so many people???.
I am confused by your OP in that governors don't launch ships, you have to do it manually. When you do you get a dialogue box labelled "Load Ship" which does exactly what you are talking about. It has a slider where you can load your ship with anywhere to .5 bil your colony ship's max capacity.
Also maybe the govern could target the next available Planet?
Target it for what? For population once your planet building colony ships is depleted?
Well, I guess this is all going to change with the new shipyards anyway. I'm still not sure how they are handling colony ships and freighters.