Delivery with Joomla 1.5.5 installation files.

Add a check if the master site uses the JOS_ table prefix.
If yes, JMS will report an ERROR to the user.
Keep jos_ as table prefix will result in deletion of all the users and therefore result in the impossibility to login into the master website.

Share the same database between Master site and Slave sites

Keep jos_ as table prefix require that the administrator backup and resotre the jos_users table each time he will install a slave site.
When the slave site is installed, the adminstrator must restore the jos_users.
If it does not restore the jos_users, the access to the master website become unavailable (due to the deletion of ALL the users and in particular the 'admin' user).
The backup/restore of the jos_users table can be performed using a tool like phpmyadmin.

If you have an existing web site using 'jos_', we recommend to rename the table prefix with another prefix.
This can be done with phpmyadmin export/import database.
When the database is exported, uses an editor to search/replace all the instances of jos_ by something else (like master_)
When this is done, the master "configuration.php" file must be edited and 'jos_' must be repalced by the new prefix.

Use a different database for the slave sites 

Another alternative consist in using another database for the slave sites and keep the master database as it is.
In this case, as the database connection is established to the slave database, the joomla installation will try to delete the users present in this slave database. Therfore, there is no risk to delete the master database users.