It is possible. In order to repudiate one of the councils, first you must wait until the Schism between Catholicism and Orthodoxy forms. Once that happens (or the Schism already happened before your start date), you need to fulfill the following conditions:
-don't have a regent
-are neither Tribal nor Nomadic
-either be the head of your religion, or be an Emperor-tier character
-don't be a heretic (making a heresy mainstream then adopting said heresy is ok for Apostolic and Coptic, but not Nestorian)
-both your religion and Orthodoxy (or the heresy that displaced it) have their own religious head
-not at war or otherwise occupied
-have 2,000 piety
-your religion has a moral authority of at least 80
-are either the head of your religion, have your religious head vassalized, or control either the County of Constantinople or the County of Jerusalem
-the bishoprics of Constantinople, Antioch, Jerusalem, and Alexandria are held by members of your religion, and none of the holders are at war
If all the above are met, you can choose to repudiate one of the councils (depending on your religion) via decision. Once the council is repudiated and Orthodoxy is declared a heresy, you can then enforce the other council to absorb the other non-Catholic, non-Orthodox branches of Christianity once your religion controls the required bishoprics, and can absorb Catholicism if you control all five sees of the Pentarchy. Note, however, that a character can only do one of these things in his lifetime. You will need to go through at least three characters to completely unite Christianity.