Even though most people may just see Murdoch as a normal dude, the Walsh kids recognize him for what he really is—a savior. When Murdoch enters their lives, his presence makes Nikki more bearable and normal for a while, which is a huge deal for the kids, who are used to pure chaos on a daily basis:
I even began to take for granted the way our mother was during that time. Soft. Laughing. Warm. Reasonable. (8.22)
And even though things get tough when Murdoch breaks up with Nikki, he doesn't hesitate to help the kids out when they come to him for help. He doesn't turn them away and act like their problems aren't that big of a deal, and instead, he immediately takes on the responsibility of contacting Aunt Bobbie and Ben and working with them to make sure that the kids are in a safer situation:
I was grateful to Murdoch, who kept in touch several times a day, even though he was having his own problems with Nikki. (45.10)
Murdoch doesn't have to do any of this stuff—the Walsh kids are just his ex-girlfriend's children, and he has no obligation to help them out—but he takes time and energy to advocate for them, and even puts himself in dangerous situations (since Nikki is a serious stalker). Even after Nikki loses custody, Murdoch continues to check-in on the kids. He becomes like another parent—or at least a guardian—to these kids.
Murdoch is no angel, though. The reason that he connects so much with the Walsh children is that he has his own difficult past. He was once an abused child, too, and he totally gets where the Walsh children are coming from… especially Matthew. He even understands Matthew's dark urge to hurt Nikki:
"I haven't killed anyone since I went after my father at thirteen. I won't kill anyone again, even when I believe they deserve it. But still… yes, you found someone who could have killed your mother. I just—I wouldn't. I promised myself. I'm sorry." (53.63)
When Murdoch intervenes and stops Matthew from killing Nikki, he does so because he knows where Matthew's anger comes from—he's felt the same thing toward his own father, and he killed him out of anger and desperation when he was thirteen. Murdoch knows that Matthew sought him out because Murdoch does carry that darkness inside of him, but he's been doing everything he can since he was a teen to banish it. Murdoch doesn't want to be the boy who killed his father anymore; he wants to be able to live his own life.
And because Murdoch killed his father, he is perhaps the one person who would not judge Matthew for having such dark and violent desires. He doesn't think that there is anything wrong with Matthew, or that he needs to be rehabilitated—Murdoch understands. But at the same time, he knows the emotional consequences of carrying out such an act and is able to stop Matthew from making the same mistakes.
He doesn't want Matthew to have to go through the same dark and complicated anguish that he has. And in intervening, he helps Matthew have even brighter prospects for his future.