There are several cases of the different temples working towards their own goals, often without telling each other, or, sometimes even the imperial government. Take, for instance, Meh'Lindi's surgery in the Inquisition War series. (Written by Ian Watson, great series by the way, I strongly reccommend it to anyone who has the time. Get the Omnibus) The person who performed the operation was eventually marked for (unsuccessful) assassination by his own temple.