This is more of a general comment than a suggestion for a replacement, but having just returned from the International Computer Music Conference, there's a strong dissatisfaction with the usefulness of Lilypond as a music markup language in that community, so almost nobody uses it. At the moment the most popular alternatives are proprietary ones (Finale and Sibelius), but the long-term focus is on an extention to MPEG, currently being worked on by the MPEG Ad Hoc Group on Symbolic Music Representation (website at http://www.interactivemusicnetwork.org/mpeg-ahg/). Unfortunately, this is likely to take a significant amount of time, so isn't an immediate solution.

The main issue IMO is to avoid being too locked in to Lilypond, since it's unlikely to remain the ideal solution for too long (and already isn't, in many circles). Perhaps using some restricted subset of Lilypond's notation, or even a completely different simple notation of our own for a subset of its features, would allow a future migration with relatively few hassles. Allowing full Lilypond commands in wikitext would tie us pretty strongly to Lilypond though, since many of them are hackish typesetting commands rather than semantic music markup.

-Mark