ok, at point 1, instead of siliconing the side of the baffle to the aquarium, put 2 globs of silicone on either side that can easily be cut off with a blade when it comes to removal. Its more of an idea that I know would work thats in the top of my head... its hard to put into words. point 2 shows what I mean by globs of silicone of the sides of each baffle.
Wish I could explain it better...
In short: Silicone is easy to cut off with a blade, so if you decide to silicone baffles into a tank to make it a sump, silicone it in a way that would be easy to get at with the edge of a blade, just to losen the baffles, then you could clean up the bits of silicone once the glass is removed.