The word that could replace "haunt" in those lines without changing their overall meaning is "revisit."
While "haunt" implies a lingering presence or reminder, "revisit" similarly suggests coming back to mind, maintaining the intended idea that the words you pray can repeatedly occupy your thoughts, especially at night.
The other options, "scare," "roam," and "interrupt," don't carry the same connotation as "haunt" in this context.