I think what your asking for is the ability to let other people take over your empire when reloading a save game, and the answer should be yes. It'll probably require manually transferring the appropriate saves to the new players, but I think it can be done -- if the devs are willing to allow it.

also, in alliance games, there could be an option to allow the allies control, if someone really has to leave and the rest wants to continue.

Giving the droped player's empire to an AI (a better one than what's in the beta's hopefully) might be a good idea. I know from other games where people take over from logged off or droped players that managing two empires/bases at once in RTS's can be a big hassel. Given Sins' complexity and depth I doubt that the job would be any easier in this game than Warcraft 3 or Rise of Nations(probably would be significantly harder).

If your going to give it to a player, my first instinct is to give it to the best player because he/she is most likely to be able to handle two empires. On further contemplation though, the player the computer ranks the "best" on a team is likely already have a large empire thereby creating a bigger management problem for that player than say the worst player. So I'd probably have to say the worst guy should take over if you're not going to have an AI take over (also the worst player would be the easiest to kill, in theory, so if he dies then he has a back up empire for a second chance).

It already hands it over to the AI if you quit. You can't rejoin the game in progress, but if everyone else then quits, the group should be able to resume from a save and you can get your spot back, AFAIK. Worst case, you can resume from the last autosave prior to your drop.