If past history is any indication, Kontakt 6 should peacefully co-exist with version 5. At one time I had four different versions of Kontakt installed and never had an issue, as long as
I didn't get confused about which version I was inserting into a new project.
The Kontakt player itself, AFAIK, is self-contained and does not install any other DLLs that might result in a version mismatch. I've just now verified that assumption with Dependency Walker.