Hey Farzad,
Sorry for the late reply. I'm the person maintaining Cloverage, so I figured I'd share how I'd proceed.
Is it actually necessary for you to run Clojure tests via Junit? Cloverage works by instrumenting forms, so it has Opinions(TM) on how it wants to be run. However, most coverage tools should support similar output formats; Cloverage for example supports a plethora of them. Many of these formats support being merged by third party tools. Sometimes that's e.g. coveralls/
codecov.io as a target.
so; TL;DR: maybe turn the problem on its head, don't try to run them simultaneously, run separately, merge later? (Effectively a similar approach to what you'd do if you had e.g. a "fast" path that uses an optional dependency and a fallback path and still want to get perfect coverage.)
hope that helps,
lvh