No. Those are not the dead worse thing you can deploy in an enterprise, because we have many customers who have this deployed and working currently.
You didn't say if there was a firewall between sites.
You didn't say how often radius timeouts are occurring.
You didn't say if you looked at the Clearpass event viewer to see if there were any errors that corresponded to the timeouts.
Your post is not detailed enough to make a coherent assessment about what could be going wrong. You could have answers to the points above, but they must be answered in the course of looking at your issue, because they could all be factors.