The purpose of all the WEAPONS in FF7 is to free up the mako energy to be returned to the lifestream. No more, no less. Shinra happened to have large stockpiles of the stuff in the reactors, which is why Sapphire and Diamond 'went after' them.

After the Gem WEAPONS' jobs finish, then Omega's turn comes in. What is done with the lesser weapons is unsaid, though it would make sense for them to convert themselves back into raw lifestream for the spaceflight.