To be fair, it's basically confirmed in Heavensward that the Primals aren't really gods in the traditional sense. They are mere aetherial constructs made in the image defined by their worshipers. The mental state and beliefs of their summoners changes how they appear, and what they might wish to do. Titan has been said to be summoned both as a protector and a violent monster, depending on what state the Kobolds were in. This is shown in game with the sidequest that had the child Kobold angrily and nearly accidentally summon Titan, who acted differently than usual. It's not really surprising or even paradoxical that the Eorzeans can support religion but disallow summoning. After all, worship of the twelve has never involved summoning as far as we know, and they wouldn't see a conflict there.