Why don't they just build the gates and add some pumps to circulate water between the lagoon and the open ocean?
2) Venice Laguna is huge, I don't think that could be feasible
As for the size of the laguna, they're talking about walling the whole thing off so some circulation pumps shouldn't be too much of a stretch. Alternately they could install some kind of bubbler system (like a giant version of a fish tank air pump) to keep the water aerated in situ. Again, it's not going to be pocket change but it's an option.