Hi,
The idea to repair this NTFS "feature" to update a folder modification time every time when changes the folder content is fine itself. However it seems, that the latest file modification date does not always suit as the folder time.
Would not you consider alternate approach: let Multi Commander keeps the original date of the folder when it adds, deletes on renames a file or subfolder in this folder. Technically it should mean, that before starting any file operation in a folder, Multi Commander records for itself somewhere the current value of the "modified" attribute and when the operation is finished MC should restore this original value.