If the value of the href for Canonical tags is populated via javascript function, would that affect the Search engine indexing (as search engines ignore javascript) ?
I'm not sure I fully understand the question as you worded it. But here's my take:
Canonical tags are used to make sure that Google (et al) knows that the same page with different URLs are, in fact, the same page.
This saves Google a lot of processing time, because it will treat those pages as a single page instead of trying to index every one of them. Also, your domain's search engine ranking will probably go up because Google doesn't think you're duplicating content.
For any page that could be duplicated because of parameters, you should include a canonical link of the page you want known as the original. So yes, it would help in your case. Though you cannot put a canonical link on someone else's domain pointing to your domain, so putting it on a partner's page would not have the intended consequences.
If you want more information, read up here: Google Webmaster Central: Specify Your Canonical