We already have provisions in SARA to permit incidental take. A number of considerations must be followed before you could provide a permit. You must avoid and you must mitigate. You don't really have any other choice; this is what you have to do. Then, if that is the circumstance, you must be doing it in a way that is posing the least harm or having the least impact on the species. It is quite specific to the circumstance at hand and it must not jeopardize the survival or recovery of the species.
So if you wanted to dredge this particular place and it was the home of the last set of mussels, or you couldn't remove those mussels and put them in a different place and expect that they would recover, if those were the circumstances, then no, you wouldn't be able to dredge there. It sounds to me like that's not the case, but I don't have the particulars.