if theres still a problem you could have new colonies start with injured infrastructure...
I like this solution. It's not like a colony springs fully formed from the bay of a colony ship. Make it spawn at some lower level of infrastucture and then slowly build up (repair) to full. In the meantime, your fleet needs to be able to screen the planet from any siege in the area.
I don't think it will work though, at least not 100% to the extend that I think the devs is trying to prevent. I'm under the impression Ironclad wants to prevent you set foot on the planet and ultilize it too quick in the beginning, and the damage infrastructure doesn't prevent that really.
You know that right now a moderate defense pirate fleet doesn't have a lot of Pillager (as oppose to the Marauder fleet), they do have quite a few Rogue and especially Corsairs, and group of Corsairs can take a considerable time to take on with your starting resource. Now the thing is as long as the colony ship is in space it's vulnerable to all, but once it's on the planet the only thing that can hurt it is pillager.
So instead of taking on the whole fleet you can just target the Pillagers, which right now is an extreme easy thing to do. The current AI will rush whatever ship it has to your ship as soon as it's in the system, including the Pillagers. So just use your flag's ability or concentrate fire on the couple of Pillagers there, you can jump out to another planet and slip your colony ship in. It doesn't matter if your colony starts out at 1 or at 1000 infrastructure points if there is nothing in orbit can bomb it.
Taking out a couple of Pillagers and taking out 6 Rogues, 4 Corsairs, 2 Pillagers is a huge difference, especially in rush term.