Long term, this is a big issue for me: I spend a lot of my time developing Java, Clojure, and Scala code using IntelliJ so I need support for desktop Java apps like IntelliJ. For now, my customer (CompassLabs) is a Clojure shop (at least the work I do) and Emacs+swank+Clojure is a sweet combination, so Clojure development will not really be impacted because this does not require Swing desktop app support. But I am pretty much addicted to IntelliJ for Java and Scala coding.
I would be interested in an official statement from JetBrains how they will handle this issue, long term.
An easy solution is to just use my i5 Windows+Ubuntu laptop in the future.