The average user won't understand the difference. Since you're using the WhatsApp brand name it's better to add a disclaimer that you're not affiliated with WhatsApp/Facebook Inc. Heck, I would worry a Whatapp lawyer contacts you for misleading users.
I know, from an engineering point of view it's like opening a document in an iframe, but again I think the average user searching for 'WhatsApp' in the Chrome store will think it's the official app.
Current description contains their official logo and "WhatsApp is the most popular messenger application for mobile, and now it is available for FREE at the Chrome Web Store!"
