Okay, but the problem is that this places as a core principle an obligation to drive ourselves to extinction if our own happiness will incidentally lead to that as a future outcome.

We're really bad at coming up with universal principles that override all others. So it's a lot better to just not, and muddle our way through, solving conflicts when they arise, and trying to figure out which principle is more important in that context. Usually when it's made concrete in a specific case, we manage to avoid apocalyptic outcomes because we go, "Oh hey, if we reason that way, apocalypse! So I guess actually this other thing was more important."

Regarding tolerance and intolerance, I agree with you that your definition is delightfully clean and clear. Alas, the main problem with that is that it isn't the traditional usage of the word, so if you try to use it that way without giving the explicit definition first, you'll probably just be communicating poorly.

Finally, regarding leniency or cruelty under the name of freedom of religion--I think leniency is fine, as long as everyone gets equal leniency (e.g. "my religion says that a full time job is two days working and five days off" isn't going to fly). I think cruelty isn't fine. I think freedom from criticism shouldn't be a thing, but freedom from mob justice should. If pressed, I could explain why I think this will help keep us from going extinct, but probably not why this will lead to greater happiness under all reasonable metrics for cross-individual happiness.