it was using the holy language
Yes, it is of course clear that V'Ger was speaking in the "holy language" of its creator, but at this point in the film, Kirk and crew don't know that.
When I said that the primitive mode of communication could have been taken as evidence that V'Ger was trying to talk down to their level, I meant that from the perspective of what they knew at the time. From that standpoint of the film's narrative, it was a missed opportunity in not showing them trying to fit that piece into the puzzle, as part of their journey to figure out what was really going on. It would have been better to have them trying to make sense of everything by bouncing theories off of each other, instead of simply ticking off screen minutes in total confusion.