First you mentioned that you are using Joomla 3.0 with JMS 1.3.01.
Start updating your JMS with the latest version 1.3.03 before reporting an issue to ensure that it is still present in the latest version.
See the FAQ for the procedure to get the latest version.
www.jms2win.com/en/faq/faq-joomla-multi-sites#cat-122
The selection of site for deletion is normally fixed in JMS 1.3.03
The SimpleXMLElement::data() is normally also fixed in JMS 1.3.03 - This is due to Joomla 3.0 that has removed that.
Concerning the SQL error, can you provide the MySQL error description.
JLIB_APPLICATION_ERROR_COMPONENT_NOT_LOADING is a message that is displayed by joomla when calling a component (that is defined in the DB) and that does not exists anymore.
This probably mean that you have uninstalled something from the master (remove the PHP code) and that you continue to call this component, module, ... from a slave site.
So verify that you don't call anything that would be uninstalled from the master.