Re: So Bajor made one of it's moons uninhabitable for some energy
With industrial replicators it might be simply a case of at that point the Federation only had a few they could spare. Look at modern disaster relief efforts, we have resources we can dispatch and put it in at a moments notice, but it can still take time to put in all the resources a particualr disaster needs. It might be the case with these industrial replicators as well. They have x spare and who knows perhaps some of those spare were needed elsewhere.
On the continent of wild endeavour in the mountains of solace and solitude there stood the citadel of the time lords, the oldest and most mighty race in the universe looking down on the galaxies below sworn never to interfere only to watch.