I am up in Canada and my pond is being completely taken over by milfoil, and as I'm sure you know we have very little available to us in the way of chemicals. My pond is 1/2 ac. about 8 foot average depth. If I were to start over would lime be a way of completely eliminating all milfoil. If it were not for the 10 feet of rock all the way around the pond I would drain and re dig but replacing that rock is not in the budget.
With milfoil moving further north I find it frustrating that the Canadian officials refuse to look at the available science and how they can help stop or at least slow the movement of exotic/invasive species with herbicides. I hope Hydrilla never moves up there. It's here in Indiana and close to your border.
If the milfoil is there I don't see how you can keep it out for good. It only takes fragments of milfoil to spread.