I would suggest that you might be distracting yourself from more important things (like working out the details of your music language) by premature optimization. It would be better to write the simplest, easiest-to-code parser which you can first, to get up and running. If you find it too slow, then you can look at how to optimize for better performance.
The parser should be fairly self-contained, and will probably not take a whole lot of code anyways, so even if you later throw it out and rewrite it, it will not be a big loss. And the experience of writing the first parser will help if and when you write the second one.
Other points:
You are absolutely right about reference types -- you probably won't need any. Your program is a compiler -- it takes input, transforms it, writes output, then exits. That is the ideal situation for pure functional programming, with nothing mutable and all flow of data going purely through function arguments and return values.
Using a parser generator is usually the quickest way to get a working parser, but I haven't found a really good parser generator for Clojure. Parsley has a really nice API, but it generates LR(0) parsers, which are almost useless for anything which does not have clear, unambiguous markers for the beginning/end of each "section". (Like the way S-expressions open and close with parens.) There are a couple parser combinator libraries out there, like squarepeg, but I don't like their APIs and prefer to write my own hand-coded, recursive-descent parsers using my own implementation of something like parser combinators. (They're not fast, but the code reads really well.)