I had a similar issue with typesetting in theorem and proof environments; what saved me from messy LaTeX syntax was org-special-blocks. More info is on Worg:
http://orgmode.org/worg/org-contrib/org-special-blocks.html This is not *exactly* your situation, since this is using org syntax within \begin{} ... \end{} blocks, but if you can adapt your commands to be environments, this will get you what you want. -- Albert Wang
