I violently believe that Gregtech should not be designed in a way that catours to other mods to such a level that it limits itself to THEIR parameters, because other mods do not have the same implementation, goals, or spirit as Gregtech, and this is thusly a flawed and very damaging mindset.
I understand that other mods add broken, cheaty water-generators. That should be irrelevent to Gregtech because Gregtech is Gregtech, not EnderIO or Railcraft. Furthermore, those who insist on having those mods probably aren't as interested in Gregtech in the first place, so it's another case of 'why cater?' Lastly, those who really want to 'greg up' mods can and will. If water pollution is implemented as I suggested, I will disable Railcraft watertanks (which I currently use!) and other potential pure-water-generators, which is very easy to do with Minetweaker. My players won't be significantly affected installation-wise because it's just a script to add. Alternatively, one could simply make raintanks and such harder to craft- I've considered making it require sealed wood and steel or iron screws instead of just wood and iron plates. This would add some obstacle and discouragement but not remove them.
I feel that limiting Gregtech's capabilities just because 'other mods are easier' is a devaluable position that will destroy it's development and spirit both. If you remove capabilities or never implement them, you are not giving users the chocie of whether or not to use them, you are denying the choice. If you add the capabilities but allow them to be toggled, this is entirely different- They either will or won't and noone misses out. Since I feel most users would not use the simplified 'pollution = less efficiency' variable idea Pyure initially suggested, it would be a waste of time to implement which he or Asp could spend on something more productive and valuable to the community. Whereas with my idea, it would be more work but would be toggleable at master and configureable with the appeal to those who want realistic pollution, and the option to be avoided by those who would rather not use it. After all, just 'disable it' is what they would be doing if they circumvent it using another mod anyway. And if that's the route they are going to go... why are they even installing Gregtech at all?
Also, you could perhaps just have Pwater go into a centrifuge or electrolyzer or some pre-existing machine and output normal or distilled water. That would not require a whole new machine, just a new recipe. MUCh easier than my initial idea.