Actually, it is possible to operate on those files. They are database volume files, either the legacy CEDB (Compact Edition DataBase) or the new EDB (Embedded DataBase) format. There are native APIs on Windows Phone for dealing with both types of database. Of course, they just enable you to read/write the contents (databases and the records they contain) in the file - it's up to you to process those data.
Unless you have some way to increase your app's permissions (I use HtcRoot project on my phone, Heathcliff74 has a method for Samsung but hasn't published it yet), you'll need to copy the .VOL file to your app's Isolated Storage first, or you won't be able to open it using the native APIs (Error 1260/0x4EC).
You can read more about my recent exciting adventures with these APIs here:
http://xdaforums.com/showpost.php?p=22126541&postcount=102 . I was specifically dealing with the policy database, so the SMS database may behave a little differently, but the general principles should work. The links to MSDN docs for CEDB and EDB functions are here:
http://msdn.microsoft.com/en-us/library/ee489739.aspx . You'd need to write some native code, and probably expose it through COM; Heathcliff74 has written a rather fine tutorial on the steps to do that (I'm assuming you know, or can lern, C++).
Alternatively, your app seems to work pretty well as-is, so you could always just stick with that too.
Seriously, well done; this was a gaping hole in WP7's (already pretty bad) backup story.