What is the irony in so now they and their church found it necessary to deny any other sect its freedom lest their New Jerusalem be defiled and corrupted by wrong and deceitful ideas?

Answer 1

The irony in the statement above is that Puritans had come to New England in hopes of finding religious freedom, however, they begin denying religious freedom to each other.

Answer 2

The irony lies in the church's desire to deny other sects their freedom in order to protect their own beliefs, despite originally seeking freedom for themselves. This contradicts their initial intention and highlights the hypocrisy in their actions.