Well, everybody gets extra points for creative thinking here, but I believe that what I want to do is not technically possible with Sonar X2a, or possibly any other DAW, for that matter.
The problem with muting or automating volume on the metronome track as an only solution is that it will be the DAW defining where the downbeat is on the resumption of steady tempo, not me. I may be able to work with that by getting the metronome volume sufficiently attenuated in the meandering bit but not so much I can't hear it, and then "working with" Sonar's click to restart on a mutually agreeable moment. Still not ideal but it may work.
The problem with doing things in two separate takes is that it's doing it in two separate takes. The feel of the musical meandering naturally resolving back into a steady tempo may be very difficult. I'm not going to dismiss the idea of a cut and paste solution just yet though.
Thanks for all the suggestions everybody!