Where Apple is concerned I wouldn't be surprised by anything.
However, imagine this scenario. A customer buys a brand new iPhone, and a brand new Mac, together, along with a brand new pair of Lightning headphones. When the customer asks how it connects to the MacBook, they're told they will have to buy an adapter, or an optional USBc cable. So whenever they want to switch devices, they'll have to get out their adapter or do a cable swap. That's not going to go over to well.
Now I fully expect Beats to have one Lightning and one USBc, just like some have two 3.5mm jacks now to accomodate pass through. The USBc will work with everything else, and the Lightning allows pass through for sharing or charging. And the same USBc-to-Lightning cable flipped around allows the headphones to connect to either port. Nevertheless, can you imagine the Apple sales person explaining that the customer will have to do this just to unplug from the iPhone and plug into the Mac, and back, every time?
Third party headphones won't likely have a Lightning pass through making it that much more problematic as they'll have to carry a separate cable.
And I've already explained all the other potential benefits of having a Lightning port on the Mac, especially the Retina MacBook. The MBP is rumored to have 4 USBc ports, so how many more does it need?
Apple wants to make a difficult transition easier not harder. And for the Apple customer who is exclusively using one pair of headphones with all Apple gear, I can't see them doing anything that will make the experience more convoluted than it has to be -- that's the reason Apple customers buy only Apple, for the synergy. And what you're suggesting is messy, unless of course they go wireless. In which case, why offer Lightning headphones at all? And who knows, maybe Apple won't -- I just can't see it.
But again, anything's possible these days. They might even add a second pointless speaker to the bottom of the iPhone with the reclaimed space from the 3.5mm Jack. But I can't see them being that short sighted with so much at stake in this transition.