Let me see if I can clarify.
In the setup instructions for the Xen plugin (http://support.hyperic.com/display/hypcomm/Citrix+XenServer), step 1d says, "Select the HQ Agent connection (this is the agent that will connect to the Xen API, and collect metrics - so there must be connectivity between this agent and the Xen host)". The HQ Agent is where the 1.5 JRE is required, as it uses the xen-plugin.jar you downloaded to connect remotely to your Xen host's API to collect metrics.
Based on the path information you provided previously, you have the agent installed, and I assume you have it running and reporting into the HQ Server (possibly on the same machine where you are running the HQ Server). Using that agent for the Xen monitoring configuration is fine.