Oh do I know lol (maybe you already know of my ToS obsession, but I've beaten that game 14 times and I've put thousands of hours into it > > I think I need help lol)
Tales of Symphonia deals with religion, but it's a very immersive game that also deals with a lot of other topics, like the concept of discrimination, in the same way Atlas Shrugged and, consequently, The Incredibles dealt with it - the theoretical concept of, "When you make everybody special, no one will be considered special anymore", or in ToS' case, "When everyone is the same race, no one will be discriminated." (in this case, the main villain (trying not to spoil here although the game is over 10 years old so ....) trying to destroy all humans through the Exspheres and the mutations they turn humans into so they can all become lifeless beings, as a result of the main villain being ostracized because of simply being born a half-elf, something that was out of his control, but something that practically controlled his life). The religious disputes and control of the churches is just one of the main villain's many ways of corrupting and controlling the people, along with the Desians, the Exspheres, and the splitting of the worlds of Sylvarant and Tethe'alla (in metaphorical terms, the Desians could almost be considered the Nazi's for humans in ToS like they were for the Jews during WWII; and the splitting of the worlds could be considered the thick segregation and splitting of our own countries and cultures to the point that it's still causing wars today). So it's a sub-theme, but a theme nonetheless.
To answer your original post, I think the reason religion is touched so much in JRPG's is because it's such a hot topic and something that's disputed by so many people from a culture other than our own (in this case, the Japanese). The Japanese don't commonly practice one religion like those from Western regions do. They often practice a mix of different religions, commonly Shintoism, Buddhism, and Christianity. They practice Shintoism through the worshiping of Shinto shrines, Buddhism through their beliefs in the after life and the passing of a loved one through death, and some Christianity through the church when it comes to weddings and the joining of two people in wedlock (although this differs from couple to couple). Shintoism and Buddhism are the two major religions of Japan, and both of them have complemented each other since Buddhism was first introduced to the Japanese around the 6th century (while Shintoism is their oldest practice).
So I feel the reason why religion is touched so much (and sometimes so negatively) in JRPG's is simply because it's how the Japanese view the religious practices of the western world (especially because a lot of their media is a representation of how they see the Western world; did you know a lot of anime characters look so wacky and weird because that's how they see us North Americans?) and how they know it can definitely lead to corruption, due it it always being lead by someone placed higher on the religious "chain of command" (ex. the Pope), which can lead to it being manipulated in very bad and negative ways if the wrong person stands in place to represent it at such a high rank.
That's just me though, and definitely isn't the only reason it's touched so much in JRPG's 
(long post is long, sorry, getting off topic too xD""")
