That should work... I'd boil the cherries to extract the juice (if you use juice only the product becomes what we here in the U.S. would call jelly). Pour off the juice, place the cherries in a colander and mash with a pestle (back of a large spoon works). Sort through the resulting mess with a fork to remove pits and replace the cherry parts into the juice before canning. Unless the cherries are pierced the stones won't free upand float, as you've suggested.
Best of luck!