I did some internet searching and did not find anyone that had done a direct swap out. Granted, probably the majority of these replacements occurred before the existence of the internet ;-). As I am sure you are already aware (but to be thorough), modern diffusion pump designs do use synthetic working fluids.
It will probably take some fine tuning of the temperatures of the heater and cooler, but I don't see any reason why it wouldn't work. If you have means of measuring the vacuum level, you could run through some different temperatures to empirically find its new ideal operating conditions.
Worst case, the pumping efficiency will be less because the nozzle diameter was designed for higher density particles. I am not a vacuum physicist however, so who knows, it may work even better than before ;-)
Another possible issue is that it may have more backstreaming of the oil into the vacuum chamber resulting in unacceptable levels of oil contamination. Maybe the baffle you mentioned will take care of this; hard to say without some experimentation.
Just as long as no oxygen reaches the oil during operation, it wont fail catastrophically, so give it a try and let us know how it went!
Good overview of diffusion pump working fluids
Some good history or mercury as a diffusion pump working fluid