Federation is atheistic, there is no religion.
What do you think of my current signature line? Been using it about a week now.
I've not seen much Voyager, so I don't know the context. It indeed seems a bit odd for a Vulcan to use word 'prayer', even though this particular message do not seem to have any particularly religious connotations.
In any case, In Roddenberry's vision religion and superstition were things that Federation had evolved beyond, and any Star Trek where that is no longer the case is really not Star Trek any longer to me.