I'm inclined to think that Connors transforms gradually over the course of the movie, a la Jeff Goldblum in The Fly.
It makes more dramatic sense: a gradual transformation would have more tragic impact, since we'd be able to actually see Rhys Ifans do some acting to reflect the psychological transformation, and would continuously raise the stakes.
It makes more scientific sense: a man-lizard is unrealistic either way, but which is more believable, a guy who takes an injection and then turns into a velociraptor overnight, or a guy whose body slowly reacts to structural changes in his DNA, and becomes progressively more reptilian over time?
It makes more fan-placation sense: the more humanoid Ditko-version is iconic, even if you're an iPod-generation whippersnapper who doesn't know who Steve Ditko is and thinks that Spidey's nemesis is Venom, and to a lot of Spider-Man fans, the more humanoid version is the Lizard. To me, it'd be rather like the way Iron Man used the original design as the Mark I suit.