Im afraid it wont. The circuit you linked requires and analog input pin, pi does not have any. You are right, the current reef-pi ph code is tied to AtlasScientific circuit (their i2c protocol to be specific), but we can revisit that, change it to support something else if theres a compelling reason. I did a fair amount of research before going with atlas scientific probes/circuit. My finding was getting a marine aquarium compatible probe that will be used for continuous monitoring is not cheap. Atlas was the only supplier with some reputation. I do agree its expensive :-( .
I am learning electronics, and once my chops are good enough, I'll certainly attempt to address this. From my discussion with
@theatrus , it looks like we should be able to use a dedicated micro controller and to roll our own ph circuit (that does the analog voltage to ph conversion along with voltage isolation. But thats a distant future