Interesting...and I don't doubt that it may be true. We didn't witness anything like that in our time.
You definitely can't (and I don't think would want) to share the hot springs - my recollection was that it looked pretty dirty.
There is one ryoken that overlooks the onsen w/ the monkeys - the ryoken has their own hot springs, you can sit outside, and observe the monkeys in theirs (from about 100m)
It's unfortunate that many "wildlife" situations are as was described...although again, we did not see any harassment of the monkeys in our 24 hrs there.