San Andreas was named after its church.
The first Catholic church, constructed mostly of canvas, was erected at San Andreas in 1850. It was from this church, dedicated to St. Andrew, that San Andreas took its name.
Wood, Richard C. A History of the Calaveras Region of California. Ph. D. Dissertation, University of Southern California.
Given the lack of more specific records, this implies that the town acquired its name through common usage, rather than upon the suggestion of any one person. Either way, it is probably impossible to isolate a single name as being responsible, even assuming the names of those early Mexican miners are preserved.
However, Wood mentions that at the time the church was built, the Catholic population of the area was served by a French priest called Arnault. His presence in the church was also attested to in Three Years in California by the British painter John David Borthwick. Presumably, Arnault would've had a decisive role in naming his church. In other words, he named San Andreas by proxy.
So perhaps Father Arnault is the closest we have to a namer, besides "nameless Mexican miners".