Creating this was probably fun and a good learning experience, but I wouldn't recommend trying to push it beyond that point. The problem Shake solves doesn't call for the sort of DSL that uses macros to make Clojure code act like something other than Clojure code.
I'd rather have something like https://github.com/clojure/tools.cli but in reverse: a library for building, manipulating, and running command lines and interacting with the results ... maybe something that supports setting up mappings so that external programs can be exposed as Clojure fns with "Clojuresque" arguments "--rather" "than" "--arrays-of" "strings".
An important difference between Clojure protocols and C# extension methods is that protocols are one of the tools for polymorphism in Clojure, the (only?) other being multi-methods, whereas extension methods are just syntactic sugar for static methods and therefore aren't polymorphic.