I permanently left Canada in 5 June '17, so I'm a non-resident. Turbotax says that I do not qualify for NETFILE for my 2017 return. So, should I not file this year?

Just because you are not eligible for NETFILE doesn’t mean you don’t need to submit a tax return. It just means you must print it and send it by postal mail. If you are unsure as to whether you need to file a tax return, you can contact the CRA to confirm. https://turbotax.community.intuit.ca/replies/2647704