Assuming that string theory is real, perhaps there would be a very specific wavelength of energy that could cause these strings to unravel.

That would cause matter to dissipate at the ultra subatomic level and quite possibly simply convert into heat being the lowest entropy energy level available.

If I wanted to kludge that into a Sci-Fi novel, I would say that it emits string particles that are orthogonal to the strings that they encounter, causing them to break the subatomic strings.

Similar to how cern can create conditions existing closer to the Big bang, perhaps whatever reactor Powers the disruptor does the same thing when it interferes with solid matter.

You would still have quite a bit of energy release when this goes off. Anything it hits should explode roughly with the same amount of energy as if it were exposed to antimatter, but if you need to ameliorate that for story purposes then you could say that those strings then wrap around the orthogonal strings and cancel out, I kind of like how if you have a 1 kilohertz sine wave flowing across the linear line you can cancel that out with a 1 kilohertz sine wave of opposite amplitude flowing along the same line.