It doesn't matter whichever way its being dressed up: Red John was working against the BA or working with the help of the BA. Either way, Jane killed the man who killed his wife and kids. And this man was a sad and whimpering disappointment. 

Timothy Carter knew what Jane's daughter and wife smelled like the night they were murdered. He got this information from whoever killed Jane's family. If Timothy Carter is BA, then he received this information from a fellow BA person. Then we find out McAllister is this man, the head of the BA. Jane killed McAllister, the man who killed his wife and kids.

Finding out there's another Red John who didn't actually kill Jane's family would just be another unnecessary low blow. Not to mention the majority of the viewing audience don't give a crap about generic corrupt cop associations.