Evironmental pollutants is another problem we will, eventually, be able to solve. Education, of course, is a wise thing. Not just what "pollutes" but the effects these things have on the ecosystem as a whole. Understanding the symbiosis with your environment is critical in smaller environments like a small craft or even a large station. If there's really any hope of space being somewhere to go, there requires to be a deep seated respect for your environment, for it is also that of others.
In the long term, quite simply put, orbital manufacturing facilites can be sufficiently isolated as to not cause any problems with either the more dangerous things they play with, or are by-products of their use. As for the disposal of these dangerous pollutants, that which cannot be recycled or reacted into something with a productive use can possibly just get thrown straight at the sun. It's going to get vapourised with the heat before it gets anywhere near it.