These are after all standard image formats, as opposed to pdf which serves a slightly different purpose

I don't see this as so far off - pdf files can be vector graphics (i.e. eps, but without the problems you can have with eps). I do my chemical formulae in pdf as well (and even my OmniGraffle stuff) -> but for my thesis in LaTeX. It might not be necessary in every case, but it sure helps with vector data.

And to the original poster: have you tried the pathway multimarkdown -> LaTeX -> PDF?