Completing a counter-intel project makes it useless.
It sounds like you'd be better off putting a bunch of Puppet Political Party projects in the queue, with a counter intel to absorb the scraps left over.
Soon, you'll have all the enemy planets under your control, and thus more population than you can shake a transport at.
The transport minister isn't that smart. Sometimes he removes too much population from your home world until there's hardly any people left, and production suffers. It's better to control the transports yourself without activating the minister.