I'll tell you what he was thinking. Tony made it a choice for Bobby. Without verbally saying it, he told Bobby that either you kill this guy or you're a gonner yourself. And in Bobby's mind that meant that either his children would never see their father again or this guy's kid would never see him again.

That hit was based on the fact the there was a child custody battle going on which clearly upset Bobby when he was told the details.

When Bobby returns from the hit, he realizes that by killing this guy, the guy would never see his kid again. He realized that by his killing this guy, he, unlike this guy, was able to return home to his own daughter once again.

Bobby realized that he himself had come close to winding up like this guy that he just killed and would not have been able to see his own daughter ever again had he not done this hit.

When he went right over to her when he returned to the house, it was an

"Oh boy, thank God! I can't even imagine never being able to ever see and hold you ever again"

feeling that Bobby resonated to me in that scene.