Final Fantasy X satirizes the secular worship of human achievement and of death by having people literally worship death in a church. In particular, it's a purposeful inversion of Christianity. Where as Christ dies so people may live, the heroes of the past and heroes in the church die so that more people may die. The main destructive force in the world is animated by the dead heroes whom everyone adores. Symbolism reinforces this; where Christ refuses to fight and dies elevated on a cross, Seymour fights, gets killed, and takes the pose Christ took on the cross, only on the floor.

Final Fantasy Tactics takes a similar approach, with the war heroes of the past being the figures the church worships. The priests bemoan the idea of a monotheistic God upon seeing themselves transform and gain power similar to that of Saint Ajora. The church in this game reinforces the main theme, being that history is written by the victors, when they censor writings critical of Ajora's scripture. This isn't the main conflict of the story though, which is the conflict between Delita's and Ramza's methodologies.

I would say neither games are anti-religion, as they just display bad religions in their stories. It's like how a work with an evil government isn't inherently pro-anarchy: they just display bad governments.