Plumbing in the Home/Thermopile Testing
I was following the open circuit thermopile testing for a Honeywell gas valve I found here: http://www.bradfordwhite.com/sites/default/files/product_literature/44943-D.pdf
On page 12, it shows the procedure and states the multimeter reading should be between 350mV - 850mV. I was getting well over 1000mV. I had to use the 2000mV setting on my multimeter, so I'm not sure if that factored into much inaccuracy here or not.
Twice in the past, once recently, the gas control valve was showning a "gas valve electronic fault detected" error. I have a Bradford White MI40T6FBN, with Honeywell gas control valve.
First, I would check the output with another meter. I've seen some thermopile approach the 900 range but it is on those rare occasions when the pilot was excessive. These thing generate by means of heat, which I am sure you are aware, but there are some that are capable of 1000(1volt). If you are in the 800 plus area it won't hurt the valve at all but unless you have the wrong thermopile. Verify the parts and the output and retest with the gas valve off(not calling for heat)
The error you describe also has me wondering if the gas valve is faulty but I would solve one issue at a time. Not knowing the age of the equipment, I can't comment on the gas valve or the economic feasibility of replacing it.