Would have been bearable if chests dropped their contents, but they don't which makes the situation require rollback for me.
Would make much more sense to refuse disassembly.

Chests not dropping contents is on Create's end. Would do the same if a chest was disassembled into bedrock.
I don't think there was a good way to refuse disassembly with a code injection. I probably would've done it otherwise. The claims are just considered indestructible like bedrock.
You should assemble them in a compatible claim (e.g. the same sub-claim), if you don't them to break on disassembly. The claim doesn't have to be connected to the one you disassemble in.