I was thinking about making edges repel nodes in some way to avoid the problem you mentioned. I'll have to experiment some more..
I hit the same problem of crossing edges when doing this a while ago (in Python rather than JavaScript).
Rather than trying to get everything done automatically by the code I added the ability to click and drag a point. So the algorithm gets you close to a good layout and you can then make adjustments to avoid unwanted crossings.
It reminds me of an old HN comment "think cyborg, not robot" (http://news.ycombinator.com/item?id=164833).
I think that's a good idea. The force directed layout algorithm isn't bullet proof, but it's a good approximate layout for a human to tweak.