I haven't seen anything saying there is a split in the Chantry. WoT says allegiances between templars and seekers is split with some still supoorting the divine, but I see nothing of a split in the Chantry. Some of the Grand Clerics may see Justina as vulnerable, but the rank and file of the Chantry will still view her as a living representative of Andraste, you may have some who are more hardline about anti magic than they actually are about Andraste, but the only issues she will face will be from the Grand Clerics who seek to replace her, in that regard I would advise them to be very careful, Justina actually scares me in some regards.
As for his resignation, I just looked at the page in Asunder, while he does deride the Divine, he says nothing about renegotiating with the Chantry if she is replaced.
Again I feel the majority of the Templars would follow him, but I would hardly feel that the Chantry is stripped of Templars.
Varric implied it in the ending of DA 2 at the final bit of the Integration or i completely read that wrong anyway 
"Your Chantry's fallen to pieces and set the world on the edge of war"
This was confirmed to have not been the templars rebelling given he mentioned that a sentence later.
It's only a single sentence mind you, but to me if its taken at value then it confirms what Petrice stated would happen in act 3.
Schism has come.
As for the page number of when he states that, mind its only a single sentence but it is on page...413 in the Epilogue.
He states that he hopes to do so once he crushed the mage host and then renegotiate a more favorable position for the Templars in the Chantry.
Can't fault him for that.