Yep. But, there will be lawsuits and appeals for a few years, and even the EU cannot expect Apple to just reengineer an entire product line in a few months. Also, Apple isn't going to sell Lightning in one country and USB-C in another, as that will just intensify the confusion, so it will come as a world-wide release for all iPhones, which is coming one way or another — and get ready for the relentless whining because "All my Lightning ain't work with my new iPhone!"
And, even with wireless as an option, if the EU gets away with their lack of vision/innovation then USB-C will still be required. "Since we can't innovate, neither can you! It's the law!"