Conclusion
It should be obvious by now the Nikon is best at F/2.8, the Sony looks real close in sharpness at F/4, but the Sigma is another stop or two away from its best sharpness.
At F/8-F/16 all were sharp, and produced excellent 1:1 macros at their best apertures.
I wouldn't worry too much about the CA or ghosting on the Nikon, those are some extreme examples I've given you.
For Nikon owners: If you're considering a macro lens, I'd probably go ahead and get the factory model for $800. That's just me. You can save yourself about $400 by getting the Sigma and using it at F/8 and F/11, which I do most of the time anyways. Of course, I'm assuming the Nikon mount Sigma model would perform the same as my Sony mount. Also, you'd be giving up the Vibration Reduction, but it doesn't work too well at full macro anyways. The Nikon seems like a bargain at the price, factoring in the nice build quality and sharpness.
For Sony owners: The current price for the Sony 100mm macro is about $649, about $275 more than the Sigma. For the extra money you'll get a sharper image at wider apertures and more distance to the subject at full macro, plus a neat focus hold button! I'd go for the factory model myself instead of taking a chance on a Sigma, in which I haven't been having much luck with lately. But, at F/8 or a stop down, there isn't much difference, and if this is where you're going to use it, save yourself some money and buy the Sigma.