Mike, I think you have answered the question for yourself. The softare can't possibly know the difference between a button and dust! I've done much pro. retouching, both conventional and digital although perhaps a bit rusty now. What you may try is decreasing the tolerance of the dust/scratch tool so only the fine scratches get removed and leave the buttons alone. There will nearly always be something left to be removed 'by hand', however.
You could try drawing a selection marque around the figures (doesn't need to be terribly accurate) give it a slight feather, invert it and just apply the filter to the selection, thus leaving the figures and buttons intact.
Now if you want to explore layers, there are many possibilities. I should mention something here. With any retouching, make a duplicate of the background layer and work on the duplicate, leaving the original untouched. Ok, so it's a larger file but....
With layers, you can clone from one layer to another. So, you could apply the filter to the entire duplicate image, losing the buttons. What you could then do is clone the buttons from the original layer back to the duplicate. Or you could erase bits of the duplicate allowing the original to show through. Again, you could copy and paste. Select specific areas of the clothing on the background image and copy and paste on the duplicate. Not surprisingly, there are a good number of ways to achieve what you want.
I would probably try messing about with the tolerance of the tool first on a duplicate layer and expect to do a bit of manual work. I used to operate a Crosfield A2 (yes A2!) drum scanner and mount in oil. The oil (a sort of parrafin) filled the scratches but the results could be superb. It took a long time to master mounting in oil. If it went wrong, the results were often really messy. This was only applicable negs/trans.
As an aside, reflective originals would be mounted on the drum with tape. The drums revolved at a very high speed and the last sound you want to hear is a wild FLAP! FLAP! FLAP! as the tape detaches from the drum leaving the original almost in shreds at the bottom of the scanner. Only happened to me once. I had to retrieve what I could of the image. Luckily, it was not an important pic. Just a friggin boring mug-shot of a Council women.
I used my paste-up skills to reassemble the image, re-scan it and then re-touch the image. Quite a test for me. I totally re-designed her right ear but I did whiten her teeth! Nobody noticed.
Sorry Mike, I'm rambling on a bit. It's what I used to do at the printers before I was made redundant. Oh, one final thought. I guess you may know that if you are working on a Jpeg file, you lose quality everytime you save. Personally, I would save the file as a TIFF initially if it isn't already and save Jpeg when the work is done. Sharpening should be the final step also. Best of luck.