Minecraft convert block to entity form

Solution 1:

Honestly, if you are using build craft, don't bother with a cobblestone factory, just work toward a building a quarry and you will have all the cobblestone you could ever want.

When I make my quarries, I usually filter out the cobblestone and feed it in to a chain of 6 double chests and then feed the overflow in to IC's recyclers.

Solution 2:

You can use an automated miner.

You make a cobblestone generator that using pistons to push the cobblestone into the area that the autominer mines.

Solution 3:

I don't know about the mods you're using, but the piston mod that was popular before official pistons had the property that two pistons pushing a block at the same time would convert it to a resource entity; there are YouTube videos of cobblestone generators using this feature.