This one is surprisingly simple.
ANTI-MATTER.
Hit him with anti-matter. Get him to swallow a pill that somehow contains anti-matter. I don't really know the physics of how to keep the anti-matter from contacting other matter in the air, water, universe, etc., before it comes into contact with the Hulk/Banner's matter that is their cells........but then again we are talking about a world where a Hulk actually exists. Possibilities are endless.
But what's for sure, is that matter (Banner/Hulk) and anti-matter completely annihilate each other into pure energy. There would be no cells left to regenerate, or absorb radiation, nothing. There wouldn't even be any protons, neutrons, electrons, quarks.......NOTHING....of the Hulk left.
My best guess would be to do it while he's Banner, to actually get it into contact.