My answer is similar to that of a4android's; you should coat stuff, but not with "disassembler-disassemblers". Simply program your regular disassemblers to accept a stop signal and then coat whatever you want to keep from getting eaten with a layer containing this stop signal. It could either be nano sized rfid tags (which sends an actual stop signal) or a custom "nanobot antibody" structure (which physically creates a stop signal). They are to be spread evenly on the protected surface, creating a surface structure1 with the stop signal. Both the rfid and the antigen version could look, be produced, and be spread similarly, but with the following differences:
The nano rfid tag
would need some sort of power source (maybe they need a battery, maybe they could convert kinetic energy to power). They would be programmable to send various signals, such as "do not eat before [date]" or "may only be disassembled by [version of disassembler]", and this signal can be changed or turned off by a programmer (and, thus, also a hacker). They would potentially be vulnerable to EMP or other disruptive signals.
The nanobot antibody would have a fixed signal as it would be difficult to change the structure once it's been deployed. Would work as a real antibody: when a disassembler get close to the antibody, it would have an antigen which fits the antibody and, upon a match, the disassembler would leave the structure alone. These too would be possible to have in various shapes so that they can send various messages to the disassemblers. It would be more difficult to tamper with them and they would not require any power sources.
In either way, it's safer than a "disassembler-disassembler" as you do not risk that they go rogue. However, their effectiveness of course depends on if the disassembler actually respect the stop signal. If a terrorist organization want to spread destruction, they would of course try to make a version which ignores the stop signal. Whether the stop signal can be enforced or not would depend on how easy it is to produce the disassemblers, maybe only a select few companies are capable of producing them, as well as how the global standard of assembler tech looks like, although I would guess that with such technology global legislation would be that they have to be produced so that they can be stopped so you don't risk getting a grey goo scenario
1: I used the computer generated image of a lotus leaf as it was the first image I found in the public domain which looked like I wanted to show; the surface bumps would represent the protective coating while the water droplets would represent the disassemblers. This type of structure can already today be engineered and sprayed onto surfaces.