Are they using the actual Retrieve or Scan option to pull data from OE into Sales Analysis, or are they using SA's Import option?

If using the import option, the data that gets imported relies on how the transfer templates are setup, rather than the SA Housekeeping options - which are for the retrieve functions.

I have heard of no issues surrounding the retrieval of misc charges when the option is set to 'N' in SA.

There are ways to remove the unwanted data, though. One way to do this is to use SA's Archive / Purge Sales Data option. To do this, from the main SA menu, select:
4. Housekeeping
6. Maintain Archive Files
1. Archive / Purge Sales Data

Before using this function, however - you must create an Extraction rule. Actually, SA has this Extraction rule as one of it's defaults. Basically, all it consists of is:

"Type <equal to> [M]"

I would suggest making a good backup prior to doing this - even making a copy of the data and putting it onto a local workstation's drive, then test it out there first.

Regards,