I get a dialog to accept our SSL cert every time I log open Pidgin and it logs in to our Lync server.
Is there a way I can get that to be trusted / or auto-accepted every time?
No, this is handled by purple UI client. Also this is a really bad idea security-wise.
You should check where the hole is in the CA chain (look at the --debug log) and install the missing CA certs in your pidgin directory instead.
I didn't have the CA cert installed. Once I did that, it was fixed. I tried to figure out how to delete this post... but no luck.