Your work is pretty impressive. So much work has been involved in what you have done, that to remove those figures and re-base them would almost be like starting over.
I'm not completely understanding your question; "I glued them all. I only painted the based instead of texturing them." The bases do look rather thick, and I imagine that you want to get rid of them or texturize over them. On second look, it looks like the bases are molded to the feet of the figures. Is that true? What is the terrain made of? How hard is it to poke or drill a hole in it?
Kurtlg gave two solutions about how to fix your diorama, but I would use his first suggestion if possible. That would be to remove the base and put pins in the figure's feet and glue them into the landscape, because this method doesn't require re-doing so much landscape work as in his second suggestion.
I would take one figure and try the following. If it works to your satisfaction, then problem solved.
I would use a Jewlers side cutters (found in the jewelry section of Walmart), to cut the base from around the feet of the figure, which when done will make the figure look like he has a huge sole on his shoes. You can use the side cutters to trim the size of the sole down to a more manageable size then using an "exacto" blade trim it down to where it looks decent in its thickness. From a hobby store, get some tiny drill bits (they should sell a package of very small drill bits in various sizes), and either a collet hand drill or ideally, use a cordless drill to drill holes perpendicular through the foot of the soldier. It would be better if you drill into the heal of the boot rather than the instep wherever possible so you can set your post deeper. Use a small sized paper clip to use as a post, cut to size, but you might be able to find some small finishing nails that you could use, although you might have to cut off the head of the nail, so it'll work better. Take the side cutters and do a little "crimping" on the entire shank of the paper clip or finishing nail to give the glue something to grab onto. I would use superglue (probably the "gap filling'' type) to glue to post into the figure, and you (hopefully) might find that you only have to use one post on most of the figures. Now you're ready to set the figure onto/into the terrain. Simply drill a hole into the terrain, put some glue on the crimped portion of the post extending from the figure and insert that into the hole. You might want to try different glues to see what works best and experiment with how long that post has to be that gets inserted into the terrain in order to see what length of post works best to hold the figure in place.
I'd try something like this first, as you wouldn't have to re-do any terrain features or it would minimize what you do have to correct. Every hobbyist should have some Jewlers side cutters, and everything else I've mentioned, so we're not talking about much cost. The biggest expense will be your time. You said you have around 1000 figures in your diorama, so now you'll have something to do for the rest of the year! (I'm a glass half full type of guy).
You really did an excellent job in your diorama. Along with the shear scope of it, you did a wonderful job on the landscape. Removing those bases will take your diorama to a higher level.