As far as I know, there is not a way to do this. It's also kind of really strange they won't open up the template to be altered. Could you ask them for access - or just provide them the code to use?
Even if there WAS a way to use rel=canconical in a nonstandard way - I don't think you would want to do that - as it may not be supported across all engines.
http://www.google.com/support/forum/p/Webmasters/thread?tid=64f490887853e7a2&hl=en
