Too much of a good thing syndrome is very understandable. I would hand pull it from undesirable areas. It has a fairly strong stem or stalk and usually I can get it roots and all out. I'm actually introducing that and smartweed into a pond or two here and there as the alternative weeds are a complete disaster. I prefer growth on surface, open water under it. But with pondweed if you have the time and are physically able, I would selective harvest it out of unwanted areas.
