"At what point does a pondmeister intervene with natural animal events?"
Remember, you did that when the trackhoe took down the first tree starting on the pond.
But LNP hasn't been "natural" for 2-3 hundred years, arguably for 10-12 thousand. You haven't seen any wolves, woods elk, or wooly mammoths around, right?
As lmoore stated, it's all about your goals. You may have to control predator species like coons or skunks to manage for waterfowl. (Judging from gobbler populations around here, I don't think they'll hurt turkeys. But I am no turkey expert, I'm just a guy who can see 20-30 turkeys several times a year.)
You may find yourself (re)reading Dan Van Schyke's (sic) columns in PB Mag more closely. He covers a lot of game management philosophy.