I'd only do it if I had to carry a LOT of FD meals and/or had to cram several days' worth into a bear cannister. Repackaging the meals into heavy-duty ziplok bags makes it MUCH easier to pack the cannister. Just remember to take along at least one empty (cleaned for re-use) FD foil pouch per person unless you are doing all your rehydrating/cooking in the pot that heated the water.
Alternatively, punch a small hole in the FD pouch and squeeze out all the iar, them put a piece of tape over the hole. This will reduce the bulk somewhat. Note that this is what Mountain House essentially did with their PROPAK line of vacuum-packed FD meals. Those puppies are no fun trying to cram into a bear cannister - they don't compress at all!