We need to remember that Nagato himself was strongly influence by Madara's will, simply looking at the sheer amount of black rods attached to his body. This is why Tobi himself needed to check what caused a change in Nagato, who was so strongly influenced.
It was suggest a few times, that Naruto's Uzumaki-like Life Energy (or whatever he has) is what makes people want to talk to him and spew their guts out. It is likely that by sending/emanating those energies, he decreased the influence that Madara's will/black rods had on Nagato. It is quite likely that Hashirama himself was influencing Madara each time they were close to each other, which is also hinted in the recent flashbacks. This would as well explain what Tobi meant by saying that he sees Hashirama in Naruto, in accordance to changing Nagato's mind.