Okay, answering my question... I have extended ns-tracker and submitted a pull request. It's less hacky that I expected, actually reasonably reasonable.
My fork is at: https://github.com/hutch/ns-tracker
There are a number of changes to ns-tracker included. Specifically to my question, it supports the usage of load/in-ns in the way used by clojure/core.
You can use this fork in your projects by using the leiningen 'checkouts' mechanism.