That's precisely why the only acceptable way to do this is with VML on the IE side. VML is surprisingly good for something so old. It's essentially SVG avant la lettre. Its main problem is that it's very poorly documented.

Flot requires excanvas.js to simulate the canvas in IE. Internally excanvas.js uses VML.

I said that an acceptable solution would have to use VML, not that a VML solution would have to be acceptable. The Canvas API is completely dissimilar to VML, so it's not surprising that excanvas et. al. have proven to be notoriously slow. It's not clear to me why anyone would even bother, except as a way to bolt IE support on as an afterthought. Like it or not, anything that does that is going to be commercially marginal.

As I mentioned, VML is remarkably close to SVG. So there's an obvious solution here.