Uncontrolled airspace is just that, it is uncontrolled. You are not required to be under radar control. Filing an IFR flight plan would show that you are an IFR flight and where you expect to be at what time.
With regards to your comment about entering a waypoint into the FMC. I would hope that a pilot is capable enough to be able to navigate to a waypoint without needing 'the magenta line' to help him/her.
The interesting bit is that a no-fly zone has just appeared in front of them. If not talking to ATC, then how would the pilot know that it is there. If they are talking to ATC, and they are flying IFR in uncontrolled airspace, I am sure the minimum requirements are Radar Advisory?? This i am not to sure about, but the pilot has the option to modify/cancel/refile his flight plan at any point. ATC would be aware of his intentions and location.
I am not ATC, so I can only tell you as I remember, but I think all the above is pretty much correct.