So the issue you perceive is that a correctly MIME-typed .mht file has a MIME type of multipart/related -- but that for the purposes of uploading the file, you don't want to treat it as that MIME type, but rather as an opaque data file.

Just give it a different MIME type at the time of upload, like application/octet-stream. That is appropriate, if your application wants to treat the data as an opaque data stream.

But, you say, none of the browsers support user-specified or user-selectable MIME types, but rather they infer the MIME type from the file extension.  So that sounds like a bug in the browsers... but also gives an out... change the name of the file before uploading it.

The only bug I see here is your comment that the parsing fails.