They could have switched to USB-C, became standard, and then switched to one port. Then at least the head phones you but would also work on your shiny new MacBook.
Consider what would happen in that case: right now there are hundreds of millions of iPhone accessories out there that rely on the Lightning port - everything from headphones to cars to health devices and more. If Apple removed the Lightning port all of those accessories would become obsolete overnight and people would be up in arms about it (just look at the removal of the headphone jack and the storm in a teacup that became.) Manufacturers would bring out USB-C accessories for the iPhone, people would buy them to replace their Lightning accessories, the furore would die down and things would go back to normal, and then boom - Apple removes the USB-C port too.
In the space of a few years they'd have fucked over hundreds of millions of people who wasted money on replacing their accessories and the outrage would be overwhelming. People would be accusing Apple of doing it on purpose just to sell more accessories (which is what they're accusing Apple of right now because of the aforementioned removal of the headphone jack) when in reality Apple has been telegraphing the transition to wireless for a while now.
Going completely wireless would also destroy the current accessories market. No dongle or converter to fix it either.
Also apple already did change the connector for the iPhone once.
The iPhone will go USB-C because the rest of their products have. They can stay dumb and alienate their consumers, or finally start integrating with the world.
What's wrong with admitting that you took a bet and it didn't work out?
People do that all the time. Reasonable people, at least.
Removing the headphone jack had absolutely nothing to do with selling dongles and everything to do with Apple doing what it always does: seeing which way the wind is blowing and dragging everyone kicking and screaming into their vision of the future.
They did the exact same thing with the floppy drive and optical drive, they're now doing the same thing with USB and the headphone jack, and within five years you can be sure that every single one of their competitors will have made the same decision.
I had been really optimistic about the adoption of USB-C, since it is as an open standard, but the discovery of such enormous licensing revenues that are essentially without expense to Apple, makes it almost inevitable that they will begin insisting peripherals get permission from Apple, too.