That is a strange problem, since Sargassum floats on the surface and doesn't penetrate to any depth at all. If the water intake is more than 1-2 feet below the surface it shouldn't be ingesting any of the weed at all.
Similarly with the water intake, last season I inadvertently motored through large patches while at sea and didn't find any weed in my water filters when I checked - but I do avoid those patches now when I can see them.
The problem was quite big on St. Martin and Antigua windward beaches last year and the smell is ... pungent ...