If someone were to take offense to me calling them dude I would absolutely make every effort to stop the behavior. I would never want anyone to feel invalidated over something like that.
That being said I feel like this whole outrage is manufactured to rile people up. I highly doubt many people are getting worked up over it. Dude has very much become a gender neutral term and is even now just used as an exclamation. I'd be willing to bet a large portion, if not the large majority, of the trans community doesn't give a fuck about the term and they probably use it themselves.