First, getting rid of the 3.5mm audio jack is a rumor. I thought I would point this out because the OP seems to be expressing it as a certainty.
Second, there are a few scenarios here. The first, and less likely, is one where you cannot have headphones plugged in WHILE charging. That would be a bummer.
The better scenario is having an optional adapter available so that a 3.5mm port or a lightning port audio cable along with a charging cable can be plugged in. This would make the most sense.
Something some folks haven't yet mentioned (or I haven;t seen it mentioned) is for something like a noise cancelling pair of headphones we could do away with external batteries. They could just be powered by the phone via the lightning jack. So I can certainly see use for this. There is also the potential to allow the phone to be thinner (not something I care for much but whatever) and, of course, simply give more room for other hardware.
If this does become a reality, there will be some growing pains and gripes, just like with the lightning port. Cables were initially very expensive and many of use had to go out and replace cables and other accessories that we had accrued over the years in order to use our new idevices. Same would go, to some degree, with headphones. I wouldn't be surprised if that is one of many reasons behind the beats aquisition. I actually don't find beats to be as terrible as people claim (sue me, whatever). Then again, my wife got them for almost free as a Best Buy manager, so I might feel different had I dropped three Benjamins on them. I would certainly consider a set of lightning beats, but not being able to use them with any of my other devices might hold me back a bit. The fact that the port is proproetary, at least to my knowledge, would also hold me back, seeing as how that would mean we are unlikely to see it on other non-Apple products.