When I've had to deal with backups of relational data in the past (in MySQL which isn't super different in terms of capability from MSSQL that you're running) is to create a backup "package" file which is essentially a zip file with a different file extension so that windows won't let users open it.
If you really want to get fancy, encrypt the file after zipping it and change the extension. I presume you're using ASP for your SaaS and since I'm a PHP-geek, I can't help too much with the code side of things, but the way I've handled this before was for a script that would package an entire Joomla site and Database for migration to a new server.
//open the MySQL connection
$dbc = mysql_connect($cfg->host,$cfg->user,$cfg->password);
//select the database
mysql_select_db($cfg->db,$dbc);
output( 'Getting database tables
');
//get all the tables in the database
$tables = array();
$result = mysql_query('SHOW TABLES',$dbc);
while($row = mysql_fetch_row($result)) {
$tables[] = $row[0];
}
output( 'Found '.count($tables).' tables to be migrated.
Exporting tables:
');
$return = "";
//cycle through the tables and get their create statements and data
foreach($tables as $table) {
$result = mysql_query('SELECT * FROM '.$table);
$num_fields = mysql_num_fields($result);
$return.= 'DROP TABLE IF EXISTS '.$table.";\n";
$row2 = mysql_fetch_row(mysql_query('SHOW CREATE TABLE '.$table));
$return.= $row2[1].";\n";
while($row = mysql_fetch_row($result)) {
$return.= 'INSERT INTO '.$table.' VALUES(';
for($j=0; $j<$num_fields; $j++) {
$row[$j] = mysql_escape_string($row[$j]);
$row[$j] = ereg_replace("\n","\\n",$row[$j]);
if (!empty($row[$j])) {
$return.= "'".$row[$j]."'" ;
} else {
$return.= "NULL";
}
if ($j<($num_fields-1)) {
$return.= ',';
}
}
$return.= ");\n";
}
}
That's the relevant portion of the code in PHP that loops the database structure and stores the recreation script in $result which can then be output to a file.
In your case, you don't want to recreate the databases, but rather the data itself. You've compounded the issue slightly since you have a SaaS that is prone to possible data structure changes which you'll need to be able to account for. My suggestion would be this then:
Use a similar system to the above to dump the relevant data from the individual tables. I'm simply pulling all the data, but you could pull only the parts that pertain to the individual user by using JOIN statements and whatnot. Dump the contents of each table's insert/replace statements into a file named after the table. Create a file called manifest.xml or something of that sort and populate it with the current version of your SaaS application, name/information, unique ID, etc of the client exporting the data.
Package all those files into a ZIP file, change the extension to whatever you want, encrypt it if you desire, etc. Let them download that backup file and you're set.
In your import script, you will need to read the version number of the exported data and compare it to some algorithm that can handle remapping the data based on revisions you make later on. This way if you need to re-import one of their backups later, you can correctly handle transitioning the data from when they pulled the backup to the current structure of the data in that table now.
Hopefully that helps ;)