Clojure will be fine, at least. I think I remember Rich saying it was explicitly designed as a multi-VM language in an interview somewhere. Anyway, he already has an official, apparently actively maintained port of Clojure to the .NET CLR:

http://github.com/richhickey/clojure-clr/

Now porting your Clojure applications between VMs may or may not be a reasonable proposition depending on what kind of non-Clojure pure Java libraries you depend upon, but the fate of the Clojure language is thankfully not tied to the fate of the Java runtime.

I think Scala has a .NET port too, but I don't know if it's active.