Could we entertain a combination of the three options which would be to dredge the pond but use the dredge spoils to dike off the river from the pond, creating a side-channel pond?
A side-channel pond would avoid the nutrient and suspended sediment load to which any stream-fed pond solution would be subject. Such a lake has been formed on the Embarras River (tributary of the Wabash) and serves as the sole water supply of the city of Charleston, Illinois. (https://www.isws.illinois.edu/pubdoc/CR/ISWSCR-409.pdf).
In case of Lake Charlestown, the dam was left in and the lake was deepened, not by dredging but by building up the dike and pumping water from the river into the lake. The difference in water level in the lake compared to the river made increased strength requirements for the dike, which would be less at Warner’s if the dam were left in. If the dike extended from land to either side of Scout Island, much of the existing pond would remain.
Rather than take out the existing dam, replace it with an extended fish ladder, rising upstream to the elevation of the current pond. (We have, of course, in Massachusetts the Federal S.O. Conte Anadromous Fish Research Laboratory, world renowned in designing fish ladders.)
Another example is Lake Durand in Randolph, New Hampshire. The pond is adjacent to the Moose River and is fed by a stream that keeps the water level in the pond at a higher elevation than that of the river. It’s nice. Many’s the time my wife and I have skated there in the winter and swum there in the summer. Water supply for the side-channel approach for Warner’s would be groundwater flow, same as for Walden Pond and White Pond.