In theory any old MPQ editor should work, such as MPQEdit. The problem is it seems WorldEdit somewhere stores a list of all imports, which the MPQ editor will not modify. As such when you open the map in World Edit after importing with MPQ Editor it will load all the imports, but fail to show them in the import manager and fail to retain them when saving.
If one could find the file which retains the import list, or how the import list is generated, then one could create a hybrid MPQ editor which updates the import list so that imports appear in World Edit correctly.
If you are going third party editor then one might as well use a flat directory structure and archive it all only on build. This is what the StarCraft II editor does with its map components save format. Imports then can be managed effortlessly from the file system and do not even need any special handling or inclusion instructions.
