I am 99% sure Matt Cutts of Google said you will not be penalized for using the nofollow attribute to flow your internal PageRank, as you see fit. We have some more conversation on quotes from Matt on that over here.
But will it ever raise a red flag? I would be lying if I said no. I would think it could be used as a measure to see which sites are overly optimized for search engines. Heck, what normal webmaster would nofollow their internal links? Most webmasters have no idea what a nofollow attribute is, let alone use it for internal links.
So to say it will never raise a red flag and possibly lead to Google reviewing your site and then penalizing it for reasons outside of the realm of PR Sculpting, is not possible to say. In my mind, it seems like a natural step for some Googlers to look for, when bored.
Forum discussion at DigitalPoint Forums.
Note: This post was written last week and scheduled to go live on April 21st.