Put your iPhone flat on the table, look at the edges. It’s not hard to see what parts are getting the chop next. Like it or not, Apple wants iPhones to get prettier and prettier every chassis generation which largely revolves around thinness. The 3.5 mm headphone jack is on the chopping block; it’s the thickest element still standing.
The real question surrounding this rumor isn’t whether Apple would do this or not (they would), it’s the ramifications on customer satisfaction. I don’t have statistics to back this up but I would bet that most iPhone users connect the bundled EarPods headphones. Given that Apple will ship a pair of Lightning-equipped EarPods in the box, you’ve already removed the friction for a lot of the customer base. In regard to third-party accessories, it is true that there are few Lightning headphones available today. However, iPhone sales are so huge that there will be hundreds of Lightning headphones on the market, if/when it transpires that the iPhone 7 lacks a 3.5 mm jack.
It’s the classic chicken and egg problem, except with one big fat chicken.