Let me preface this by stating that I do not believe the manner in which you handled this was wrong.
However, since you inquired about alternatives......
I don't think you would have had a problem selling R1 staying on 3rd base as you description sounds that it was obvious the catcher would not have had an opportunity to put the runner out at 3rd.
The only thing that I would have done differently was discuss the situtation with your partner privately before going ahead with the coaches. On of the questions would have been his opinion of a swing.
REMEMBER, I'm not suggesting that this should have been the call, just a possible alternative way of handling the weird situtation you had.