Since your game is following a hands-off approach, your game pollution mechanic does not have to be too complicated.  You should just implement an overall, or average air quality level and once passed, the game allows the player to make a general decision.  You don't necessarily have to make it complicated and the end result (giving the player an additional challenge) will still be achieved.

Could pollution be approached as just one more threat that an empire faces? Only instead of the intensity of the threat being from outside empires or loyalty of generals, it comes from the development actions that a player takes.

I suppose pollution might affect a planet's happiness, food production, or possibly other stats. As industrial production increases additional resources must be spent on ecology to mitigate negative impacts on other planetary values. Effectiveness of investment in ecology possibly affected by technological discoveries. As such, it can become just another input for resources allocated.

How about pollution as an "overdrive" mecahnic: A planet can handle pollution fine with normally working industry, but then you are allowed to "boost" the production at the cost of extra pollution. Not for individual planets, but maybe systems or all of them at once. Then, after the boost period, you can take care of the extra pollution by lowering the production or investing in cleanup or some other way. 

Basically, have a "turbo button" for your producation when you need it, and have pollution be a cooldown/recharge period for it. It's a common game mechanic, and it can be done globally with no micromanagement.