It is wise of her to address her own reservations before they may begin to affect reality. As for your own limits, it seems that your wife and John have already pretty much gone as far as your current comfort zone allows. If she's okay with that (at least for the moment), then you have a safe space in which to do your own introspection. For the moment, things should remain where they are.
I recently heard that surveys have been done in which men and women were asked what they'd feel more threatened by, their main squeeze having a purely sexual encounter with someone else, or their main squeeze developing very close feelings for someone else. On the whole, the women were more likely to feel threatened by the outside emotional relationship, whereas the men were more likely to feel threatened by their partner having sex with someone else. It has been debated how much of this is genetic programming and how much is social programming, but the theory that has emerged is that men are subconsciously programmed to fear raising another man's child, whereas women are programmed to fear being left for someone else (and losing their source of support).
I take it your wife is nervous about both things: the sex and the emotional connection. Whereas if you were in a situation of being interested in someone, you'd desire the sex and the emotional connection together.
If you keep communicating with each other as things and your feelings evolve, you'll be able to navigate these rocky waters. Let each other know when your limits are getting a bit stretched. A little stretching is probably good exercise; a lot of stretching could cause an emotional injury of some kind. Work on your limitations gradually.
Love means never having to say, "Put down that meat cleaver!"