I don't think so. Decker says he's playing devil's advocate a lot of the time, so it's hard to know what he would've done in the big chair, but if he'd raised shields outside of the cloud, it probably wouldn't have made any difference. He might've loitered around outside the cloud longer, but once they got into V'Ger, there's a good amount of waiting around until they get to Earth, so as long as he went in at all, they probably would've been reeled in and ended up inside the outer chamber.
The real question is, would he have tried to pump the Ilia probe for information without Kirk ordering him to (since his personal connection with her is the only thing that made that work), and would he have had the big space stones to bluff V'Ger and say he knew who the Creator was and why it wasn't responding to the radio signal? I say fifty-fifty on the former, and definitely not on the latter. Decker was too conservative to paint himself into a corner that way.
