Firstly you should exclude clojure.core/>
from ns declaration like this:
(ns foo
(:refer-clojure :exclude [>]))
And then try this:
(defprotocol FooComparable
(> [a b]))
(defrecord MyRec [name val]
FooComparable
(> [a b] (clojure.core/> (:val a) (:val b))))
(def a (MyRec. :foo 1))
(def b (MyRec. :bar 2))
(> a b) ; false
(> b a) ; true