There have been a number of speculations about whether or not coffee would be banned in the Tower. This started with the banning of smoking in 1973, and many thought coffee would be next. Then, sometime in the mid 1990s, they started having articles in the Asleep! putting coffee in a positive light. You might still find some of those on the official site, unless someone took those pages off.
And, now in April, they have the KM article suggesting that caffeine is possibly addictive. So far, they have just stated that it was a conscience matter. Something tells me that it won't always be so. Usually, what happens is that local hounders and hounder-hounders will read more into it, and use coffee as a tool to judge others. Those who use coffee, tea, cola, and chocolate may be viewed as less spiritual, and be hounded to give those up. And, down the road (and especially once the Kool Aid edition of the Puketower comes out), they might upgrade it to an outright ban. To this time, I have seen nothing that says they are definitively going to ban it--but I do not trust them.
Here is the deal: If they ever do ban caffeine and they catch me with chocolate, then I am going to go out and get a 8 oz bar of the finest quality dark chocolate (organic, of course) that I can get my hands on, and then I am going to bring it right into the judicial hearing and eat it right in front of the committee. If I get disfellowshipped, that means precisely nothing since I have nothing to gain from associating with that bunch of losers anyway. And I will not be doing my body any harm: calorie for calorie, organic chocolate is actually better for you than that Big Mac or Whopper that they probably had for lunch to keep their time going in service.