Hi,
It is not clear to me if you are even talking about mojoPortal.
CMS pages in mojoPortal already support SEO friendly urls and the canonical link automatically uses the same SEO friendly url. You can also override the canonical url on any CMS page in mojoPortal from page settings.
If you are talking about supporting pages in some custom feature you made yourself, mojoPortal is not putting any canonical link in your custom pages.
In any case I've added a setting in the code today in case anyone wants to disable the automatic adding of canonical links in the mojoPortal CMS pages.
So if you are working with the latest source code from our repository or after the next release of mojoPortal, you could add this to your user.config:
<add key="AutomaticallyAddCanonicalUrlToCmsPages" value="false" />
The default is of course true.
Hope it helps,
Joe