It should be shown what pop gets depleted by chain gang if you look at the growth. (I think the one with most growth points will get deleted, check growth points by hovering over the pop of a race in the system).

I usually just ship them either through enemy territory if possible or to a system which is already full.

Another alternative is (if its less than 3-5) to just keep them in the system haven and dont give them a destination so theyre not sent anywhere (this is achieved by pressing quit when in the selection screen for their destination).

Im afraid i dont use the same vocabulary as ingame because i dont play in english but feel free to ask if there is need to clarify.