I want to mention that, currently, there are only two things colonies are good for (heavy industry for custom orders, general purpose money making) and both rely on the same stat (hazard rating) to function. Well, HI sort of doesn't, but the player is likely to be interested in making HI not be a drag on his bottom line and the hazard rating is the way to go. I would really like more unique conditions and resources that carry some gameplay consequences. Currently you just want a bit of everything on your planets, so that you can build all the resource industries and boost them with skills and cores into brokenness.
About having the player opportunistically dismantle the industry — it can be "discouraged" by simply having the option to do so from the orbit for some quick cash. That, or make built-ins impossible to dismantle, having manual disabling of them instead.