In clojure, how can I undef a var from a namespace?

If I understand you correctly, ns-unmap should do what you want:

user=> foo
java.lang.Exception: Unable to resolve symbol: foo in this context (NO_SOURCE_FILE:1)
user=> (def foo 1)
#'user/foo
user=> foo
1
user=> (ns-unmap (find-ns 'user) 'foo)
nil
user=> foo
java.lang.Exception: Unable to resolve symbol: foo in this context (NO_SOURCE_FILE:1)