For those who don't chose SWU's as one of their choice gifts and don't use JFK to fly to airports effected, I don't see how this will have any of any negative effect at all.
For PM's that chose SWU's definiately a negative effect for those that used them internationally. If a PM flies a long haul on a LUT fare, could be a positive or a wash.
For me as a DM this will be a positive change IF I can use the SWU on a cheap domestic ticket. My wife and I usually take one international pleasure trip a year and if I can upgrade both of us on a low fare it will be a big savings.
For non-rev's on the JFK routes this is definitely a positive. For non-revs flying to Hawaii from LA, definiately a bad thing. For non-rev's on international it will mean no PM's being able to use the SWU's internationally and fewer for diamonds but more diamonds may be using them now that they can be used on any fare except an E.
IME, it is cheaper to buy a discounted J fare than a B or Y fare and I don't have to play the game of finding a route to use them on and typically don't use the SWU's for my one gift. For next year I probably will unless there is a lot of Sheena reported with people not being able to use them.