The Kona Cafe always offered the 100% Kona by the bag and in bean form, at least in the last 10 years or so, both in the restaurant and at the counter for walk-ups. It was always expensive, though. (About $40 for a one-pound bag.) Probably from Joffrey's then, I guess. So, it should remain, it would seem.
As for other coffee on the resort, it was better when it was Hills Bros., but as I noted above, I believe that was lost when Nestle sold its Sara Lee division (which owned Hills Bros. and most of their other coffee lines, except obviously Nescafe). Since Nestle is a major sponsor of WDW, that is probably why everything changed over to Nescafe (Nestle's primary coffee brand remaining).
I wonder if this wholesale dropping of Nescafe coffee means their sponsorship contract with Nestle is history also?