"Original "Contact Seller" functionality will be replaced with Instant Messenger plugin. This means that instead of sending mail to seller, message will be sent and seller can see this message in it's profile." <--- from plugin config.
I have here also problem, when Replace Contact Seller Functionality turned on, seller receives 2 emails
1) standart native email. (bad)
2) messenger notification email about message (very good).

Yes this emails cannot be turned of from plugin side. You may rather replace contact seller button with send message button of plugin.

send message button of plugin redirects to other page..
so better is replace contact seller functionality.
how can I turn of that emails?