Ady,
CleanWord in FreeTextbox, FTB and others we tested don't exhibit this problem. So CuteEditor shouldn't either. Clean means clean. If the current default settings use DIV, br or whatever, the clean function should abide by it.
Respect the end-user and don't look at this from a technical viewpoint. Users are NOT expected to have to spend a ton of time cleaning what is supposed to be clean.
Look at editors that actually import Word docs - like Googel Docs - and not just paste them. Do you really think developers would buy the product and people would use them if they weren't as close to the original as possible?