What you guys mentioned regarding terraformers versus transcendentalists is indeed more or less what I'd like to reach. A polarization between and - if the Flowering Counter reaches high levels - a big showdown between the pro-Planet and anti-Planet factions. This is what I meant when I said Planet should have more teeth than it had in SMAC, where you could run what was by all possible roleplay definitions an ecologically disruptive playstyle without Planetmind giving any actual gameplay problems. The trick is in finding some way to do this without it becoming a game of whack-a-mole, as some people have commented fungal blooms currently are.
At the moment I don't think religions are the way to reach this polarization though. The problem is, while pro-Planet easily lends itself to a religion, anti-Planet doesn't. Can you consider the Hive or Believers individualists? So "transcendents vs. individualists" doesn't really work.
I was thinking of creating a civic category called "Ecology" containing three options (besides the default one), which would have a large effect on diplomatic relations (the higher the Flowering Counter, the bigger the effect would become).
1) Hybrid: the pro-Planet option. Should have some synergy with fungus, and with having many small bases
2) Terraformation: eradicate Planet, and replace it with a terran ecology. This civic should favour building condensers, boreholes...
3) A third "neutral" option. Not sure what to call it. Basically you'd chose to not interact with Chiron's native ecology at all, and neither try to impose a terran ecology. Rather all people would live concentrated indoors in bases. All food production would happen in greenhouses. No contact with the outside. Something like Biosphere 2. This could have interaction with a specialist economy. You wouldn't be able to build farms, forests, condensers, fungus etc.
The trick is in trying to make the AI realize the importance of this civic category.