The reason I'm doing a little research on this gentleman is that there used to be a baptism font in the RC Church in Listowel, Co Kerry with an inscription below which mentions his death.
In memory of Surgeon John McDonagh Stokes
Who died at Peshawar during the mutiny.
His sorrowing sisters have presented
The Royal College of Surgeons in Ireland have recently told me that he died in Rawalpindi in October 1859.
I'll check out the Times for an obituary, thanks for the suggestion.