Well you're typically not thinking of a compilation step with Clojure.. so I found the original question a bit not-applicable
The goal isn't to introduce .. a compilation step? but to have the program blow up in the spot where there is an type mismatch. If you don't use a protocol you may not blow up, you may generate a nil, and you may blow up much further down the line (or not at all)
In the rare instances where dynamic types cause problems, they're virtually always something convoluted like that. The protocol design pattern describes the interface and protects you from hard to debug situations
In my experience (mainly when trying to understand the implementation of core.logic), the problem with protocols is that the code inspection tools choke on them.
For complex data structures I typically just hide details behind a protocol and deal with the set of interface functions.
You can then freely mess with the internals and not worry about details