Well, that would spoil the fun somewhat wouldn't it?How about adding a "Auto Disembark" option in the right hand panel, so if a fleet carrier jumps away when you are not online for some reason your ship will exit the carrier.
If you really want the carrier when you log back on (and assuming it does not go away), just log off in the carrier instance - but disembarked.Or
Maybe you could just not park on a carrier before you log off...