Your comparison of Wizard with Refine is misguided. The two products do completely different things. Refine "refines" data into a usable form. Wizard is a stats and visualization tool for understanding an already-clean dataset. Last I checked, Refine actually runs a local web server, even if its client is in the browser, so it's not that different from a native app. Wizard also does incredible amounts of visualization that Refine doesn't do.
(disclaimer: I purchased Wizard a few months ago and have been exceptionally happy with it -- it's a brilliant product)
So, pair Refine with d3.js and you've got both. There's no reason I see to require native application for data visualization unless you absolutely need to load enormous amounts of data, but the value in the visualization itself tends to diminish the more datasets you shove in it. d3.js has very powerful visualization tools https://github.com/mbostock/d3/wiki/Gallery. He chose to build is tool in the native Mac platform, which is great, and great to hear the product is really useful for you -- I'm just defending against alternative tech choices. If you wanted to build this in web tech, I think you surely could. I'm not saying it should be built in web tech, but I disagree with the notion that it couldn't be built in web tech.
(disclaimer: I purchased Wizard a few months ago and have been exceptionally happy with it -- it's a brilliant product)