Ok, so the hack thomas.behr suggested still works! Here are the exact steps I followed. Variations may also work, cannot comment.
1. In terminal,
$ cd ~/Library
$ rm -rf yWorks
2. In Finder, go to Applications folder and delete yEd.app
3. Download latest .dmg file from yWorks and double-click. This will mount the file (appears on desktop as a drive). When I do this, the installation procedure pops up a window that offers to drag the yEd.app to the applications folder. Don't drag it yet! Instead, double click on the yEd app.
4. Having cleared all the previous links, now yEd apparently has a fresh start, and the white-screen-of-death no longer appears. Make a new file, test it out, save it, etc.
5. When you reopen, yEd still works. Now you can drag the yEd icon to the Application folder as normal.
Whew, what a hassle! But yEd is such a great application, it is worth it.
