If you want to take the author's ideas to a logical (and in-the-book RAW) conclusion, a troupe can ignore each and every rule in the book if doing so makes the game un-fun for them: Lords of Men, pg. 125 (I think - it's about Incapacitating damage, and what to do when PC's get killed.) Which, in turn, is just a re-statement of the "rule 0: have fun" rule, which I think is in the core rulebook somewhere. So, yes: if it doesn't work for your table, then it is RAW to ignore the rule.
That seems to be what the author was talking about. For him, teaching Gentle Gift isn't fun for his troupe, so he'd have a problem with it. But the rules don't explicitly disallow it (as he had a chance to do when he was writing up the list of "allowable virtues," but decided not to include it), so it's a troupe call (like everything else). He just was part of setting up the framework, and it's up to the troupe to decide what the consequences are, via storylines.
However, responding to each and every rules question with "go with what is fun and ignore everything else" is not an answer to a question about the rules. If that was the case, then the core rulebook would be significantly smaller and less useful. As Jonathan said - here on the forums we only have RAW - we aren't a part of each other's troupes, so we can't claim "X is wrong" - rather, we can say only "the rules say X, and for our troupe we've done Y".
And we've got the rules saying "you can teach Hermetic Virtues" - Gentle Gift is a Hermetic virtue. Therefore, you can teach it. We've also got the author who wrote that saying "I'd not do that, but instead of prohibiting the ones I didn't think were appropriate I decided to write out the framework, and let everyone's troupes determine the consequences for themselves".
(And on a side note - if you're going to fully integrate Gentle Gift as opposed to simply have folks teach it, it's probably not necessary to use the Hermetic Research rules for it - I believe that, since Gentle Gift occurs naturally, you can use the less-Warp-inducing Integration rules, instead. Ie, the ones listed in Ancient Magics and Hedge Magic, rather than the ones in True Lineages.)
EDIT - that being said, if the author of the book says "I'd probably not do that", I would personally take a long and hard look as to why he said that. As Jonathan mentioned, getting rid of the Gift penalty significantly changes the game. Now, if you WANT to play through that (as had been mentioned, either through natural selection, or as an experitment in alt-history, or whatever) then that's certainly up to the troupe. But I happen to agree that everyone having the gift would radically change the Order - to the point where it probably wouldn't be recognizable as the Order any more. If that's what you want, then go for it - but it's definitely a high-level, genre-changing event.