The main reason I think it was missed in the film is because in the Star Trek universe, ultimately the transporter is safe when operating as intended. McCoy's concerns about having his molecules scrambled are treated as an eccentricity, and the fact that TMP treats them that way is really my exhibit A that the film missed the connection between the transporter and V'Ger.
Which is an interesting point in and of itself about TMP, actually. Here you have an absolutely horrific, gruesome accident involving two people being killed by the transporter. And then, just a couple scenes later, we're back to making jokes about cranky old McCoy and his attitude toward the transporter. Seems like an inappropriate time to be laughing about his attitude, and certainly his fears would seem more justified at that point.