I want to kind of add a disclaimer to my question. At the limits of course I am not questioning ecological conservation - the Earth would both suck if it only had humans and our crops and livestock in it, and be thrown completely out of equilibrium so that it would suck for humans too. But I assume that the effect you're talking about is where over time some tiny little place becomes bad for some species, so they stop going to just that one place. Likewise you mentioned the opposite effect where "It can also create ecological activities, where some species congregate around the outlet because they want the hotter water" but this doesn't seem like some objectively great thing - wow, we have all these fish hanging around what amounts to a thermal spa for them, fantastic - but more like just a neutral fact.
This is my impression, that it is what it is, so I'd just like an explanation of the strong moral component or why this is important - since you seem to understand this. (Again, I can do part of the reasoning myself since obviously I wouldn't choose a barren lifeless planet with only humans and stuff we eat, on it, I'm just having trouble extending this reasoning to tiny local perturbations.)