Unfortunately, Bean’s revelation does definitely poke some holes in other speculation regarding the character, especially the folks who believe he warged out of his body to survive.
Sean Bean said Ned Stark’s final moments were spent praying, although he admitted he kept wording vague as he didn’t know if that was actually a thing.
Luckily for Bean, Ned’s observance of the Old Gods of the Forest falls within the character’s canon, so it’s not like his revelation just destroyed everything fans knew about this Game of Thrones character.
Bean’s quote also seems to imply the decision was his to implement the silent prayer, which would drastically decrease the chance the words are relevant somewhere later on in the series’ plot.