As others have pointed out, it's s-expressions (and possibly simply scheme) so reading and writing shouldn't be difficult. If it uses scheme comments, those will be a problem just as when transforming any programming language. I the other hand, if they syntax supports doc-strings, you're all set.

Add far as AST visitors, you're probably better off with XPath/XSLT tree transformations. (Anyone know of a suitable library?)

On the other hand, the don't-swim-upstream approach would be to use one of the best programming languages in existence, Scheme, you do your config management tasks directly, rather than an arm's-length parse, modify, write approach.