As a player, I'm surprised that the Thieves admitted that they kidnapped the Cleric b/c they were worried that the temple might come after them.
What possible reason could they have for such a concern unless they are either working with or opposed to the temple's interests?
In fact, they were so worried that the Temple might come after them that they risked kidnapping one of its priests who was snooping around, which is curious since that act would normally bring the Temple's attention to them.
More questions than answers, but in R.L. my gut would be conclusive that they are involved with the outbreak, possibly even working with foolish members of the Temple who might increase their power and influence by appearing to put down the invasion and save the City.
While the second part of the projected scenario seems unlikely, I can't rule out the possibility. The first part of the concept seems almost a lock to be true!