I doubt this will happen but I think this could be an interesting development in the manga, because it would mean Ganta would become the new villian.
In my head the Woodpecker personality is the reverse of Shiro's Wretched Egg personality. I think the series emphasizes that the Wretched Egg is the mature aspect of Shiro's personality while Shiro herself represents "innocence." The Woodpecker I think will be a more of childlike personality.
The Wretched Egg tells Shiro that she hates everyone and everything that is she wants everyone to share and feel her pain. The Woodpecker's perspective is more like that of a very cruel child. When the Woodpecker hurts people it's not because he hates them, but he is simply a child playing with his toys.
Here are some more theories about Ganta's past:
Shiro/Wretched Egg did not cause The Great Tokyo Earthquake, Ganta/Woodpecker did. This theory is admittedly pretty extreme and I expect it to be shot downlike a lame duck during the flashback/memory transfer chapters, but let me explain my reasoning. Ganta has shown to be an extremelly powerful Deadman whose abilities at times surpass those of normal Deadmen and it has been implied that he is as strong( if not more so) than the Wretched Egg. From what has been revealed, Ganta was not infected with a unique Branch of Sin like the Forgeries or special forgery unit one, but with the original nameless worm.
Part of the theory stems from Shiro/Wretched Egg herself. The Wetched Egg has been shown to be powerrful and destructive, but not nearly to the degree from 10 years ago. Toto/Mockingbird thinks this is because The Mothergoose System is retraining Shiro/The Wretched Egg's powers, but what shoots down Toto's theory for me is how unrestrained the Wretched Egg is. She can still cause mass destruction, was able to travel a great distance to murder Ganta's classmates and wipe out an entire military unit.
The theory I have for why Toto believes the Great Tokyo Earthquake was caused by Shiro is that she tried to protect Ganta by making it look like she caused it.
The Mother Goose system is meant to restrain the Woodpecker, not the Wretched Egg this is admittedly one of my most far fetched theories, but let me explain my reasoning. The Wretched Egg has been shown to be awake at times when the Mothergoose sytem is still on. After Shiro chooses the death called maturity (what I actually think is happening is the Shiro personality and the Wretched Egg personality are fusing) The Wretched Egg is able to still go on killing rampages. I think the Mother Goose system does affect her, but it main duty is to restrain the Woodpecker.
A scene has been developing in my head since I read chapters 44 and 45.
At the last minute before Toto's mind totally takes over Ganta's body, the Woodpecker personality emerges and violently hurls Toto back into Mockingbird's body. During this process, the machine Ganta is in breaks apart and he quickly gets out. What follows is a violent conflict in which Ganta's Woodpecker abilities start to emerge. During the fight, Shiro comes to Ganta's aide and the Wretched Egg personality starts to emerge. At the climax of the fight the Mother Goose System is destroyed and the wretched egg personality completly emerges and starts to wreck havoc. During this time, as Deadman Wonderland starts to fall apart and the two Shiro personalities fight for dominance Ganta, having learned about what happened to Shiro in the past and his role in it, apologizes for the pain he caused them/her. As a way to show his love/apology for her/them, Ganta tries to save them both at the cost to himself. What follows is everyone's mad dash to escape from Deadman Wonderland that is quickly falling apart.
In the escape, it looks like everyone (including Shiro) except for Ganta survived. However, on the edge of a beach
Ganta's body is found by a few Japanese locals. A few hours later, the Woodpecker wakes up after examining his
surroundings he begins to laugh.
The story arc that follows is essentially Ganta/Woodpecker on a rampage.
