Looking at everyone's conspiracy theories, made me want to add my two cents. 
My theory is that its not a conspiracy. Hear me out....
I mean I get it the chantry is spread all across Thedas, its one of the most powerful military powers in game. But, I've always seen it as well, more than a little incompetent. Or at least more interested in preserving itself and its own authority to the exclusion of anything else. Hence the Dissonant Verses.
E.g. The elves fought against Orlais, punish them by making them permanent wanderers, and get rid of the part of the chant that says elves should have a home and say its the Maker's will.
Mages are dangerous, we need the power to lock them throw away the key, and only let them out only when we've got Qunari that need burning. Get rid of the part of the chant that hints that maybe mages weren't completely responsible for the blights.
My issue with the chantry is this, instead changing themselves so they are in line with the maker's word, they change the maker's word so its in line with their ideology. Changing the chant for political expediency doesn't lend you any credibility when you're claiming sole jurisdiction over morality.
Phew... rant over.