Jim Dalrymple, who knows his music and doesn't want anyone messing with it, brings up this point on The Loop:
If you look at the way Apple typically does things when introducing new technologies like this, there is no reason you wouldn't be all for this new plan. They make it better, not worse.
I would fully expect that if Apple did implement this idea, the audio would sound better through the Lightning connector than the older headphone jack. Not only because Apple can add technology to the chip (noise cancelling, etc.), but because the headphone jack is not very efficient. It's been around forever and hasn't really improved how we listen to audio in a long time. A fully digital connection would improve everything.
Other companies, including HTC, have experimented with removing headset jacks before. If Apple does go 3.5mm-free for the iPhone 7, I expect it'll be for exactly the reasons Jim cites: better audio, and reclaiming the room inside the casing the current, 100-year old jack takes up.