I'm not saying Skyler is doing the right thing by cooperating with Walt, but her reasoning is to help Hank and Marie (since any money that reaches Hank must be 'clean'). And yes, Jesse obviously has a soft spot for kids, as we saw in the 'Peekaboo' episode and the one with his younger brother. My interpretation is that he doesn't want kids to end up like him, so he is trying to protect them—or, as you said, act as a father figure.