GEF is neat, but it's more concerned with layout than with actual bit-wrangling. I noticed in my own work that the lines connecting nodes in a graph weren't anti-aliased and so looked very jaggy. I searched the Eclipse forums and found other people recently asking about this, and some vague replies that somebody "might work on GL and/or DirectX support". So the answer is no, not now.
There's an article at
www.eclipse.org about using GL with SWT, and I have wondered how hard it would be to just use GEF for layout, but render things directly using GL. Haven't tried it yet, though.