The Church wouldn't have anything to gain. With them out of the way, whoever is controlling this Esper army might have control of the entire world. We know the Church and magicians are far older than any organized group of Espers. They mentioned in Index that the two factions are at a balance of power, and a certain individual who began to develop a third faction after meeting a certain someone else. This group mixed both magicians and espers. So at the time (a few to several months past this event), both sides believed there was a stable balance.

Perhaps the faction in control of the espers was secretly building an army to finally tip the balance their way.