It sounds like you are thinking of adding a meta nofollow tag rather than a rel=”nofollow” to the ‘switch to desktop’ link?
When I first tested the plugin on my LG phone and did a search on Google Mobile for my site, Google used it’s own formatting and ignored the plugin by default. So I never considered that.
I’m assuming Google can still travel through the site and see the proper mobile headers without following and indexing the wpmp_switcher=desktop type links.
Sorry if I came off harsh, other than the duplicate pages being indexed by Google, it looks like a great plugin.