The stuff we do under-the-hood would make this relatively simple to implement. We already have a custom, intermediate, math expression language which we use to hold scanned data. One would only need to write a converter from this language to latex instead of the visual typesetting that we display on-screen
I'm betting that interpreting your math handwriting would be quite a bit harder than interpreting printed text. That said, I'd love to have that feature, too.
I'm halfway through a thesis, so it's too late for me, but others could have a notorious learning curve eased somewhat.