Yeah, it's only not "canon" if it breaks seriously with continuity, in an absolutely unreconcilable way. On quality grounds, if that worked, I'd "decanon" Enterprise, most of Voyager, and half of Next Gen.
Way to Eden seems to me like something that might have been more respectable on paper. I like the idea of the leader's disease, where he has to stay within civilization, but he resents it so much he forms a cult to deny and escape his predicament.
It was brought down by the out-of-touch, silly, Hollywood depiction of the counter-culture, the outfits, and an anti-counter-culture "moral" at the end, warning kids not to be led astray by clever leaders who don't value their sunjects' lives, which come to think, is a valuable message... and I suppose that if you combine that with Spock's support of what they were about, the rank and file 'hippies' that is... maybe it was a balanced message. Still, it comes across as a horror story about how horrible it is to be a 'hippie' (as if anyone on ST knew what that meant).
As for our not having a choice as to what's "canon"... screw that. There WILL come a day when something so awful is made by Hollywood that it can't be accepted by most of us. Then we'll break ourselves of that feeling that if it's onscreen it's automatically "Star Trek". Legally it will be, but if ST gets perverted enough by clueless people in Hollywood, we'll all wise up and say no, ultimately this belongs to us.