You did try escaping the comma with dashes like this \, did you?
- it works with Gmail headers but won't work as good with Yahoo's and likely some other mailers that still treat the comma as separator...
Afawk, the Outlook had a special feature that could be enabled to encode the comma in from: headers properly meaning in theory that should be possible.
The problem is, however, even if there was perfect way to escaping the comma, the cart would still place that Store Name altogether into a subject of most notifications and show the garbage with all the special characters out there in an unpleasant way...unless you go the hard way and replace the %s placeholder by fixed plain text wording in all the notification subjects via the system's localisation Languages Definitions...
Implementing the Owner Name for the From:s of the cart could save a lot of hassle.