We have three installations of SCCM (Config Manager) 2012 and need to change the service broker ports (SQL Server 2008r2) on them. During installation two of them were overlapped. We've explored this a variety of ways and haven't landed on the best method to do this.
I believe you can just change the port that is needed. SSB is a SQL side process and not a ConfigMgr port, you can just change it back if it does not work.
You cannot just change it though, I think you have to drop and recrete the broker endpoint, you can use this command to drop the endpoint.
You can then use this command to recreate it:
Always worth a test in a lab environment though first and a backup of your ConfigMgr site.