I have made a slight modification on the CRM 4.0 Sdk plugin registration tool. I simple added a new property and once checked default credentionals are used when connection to discovery and crm webservice. It's your own choice now to either user current user credentionals or someone elses.
Simply replace attached files and recompile your plugin registration tool as described in \Crm 4.0 Sdk\sdk\tools\pluginregistration\readme.doc
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