There's No Moral Dilemma...
People are looking at this from the wrong frame. They merely consider whether or not this girl would have a better life with her well-off kidnappers versus her absentee mother. That's a false choice. Even if THIS girl is better off with Freeman, the fact remains there are other children in need of stable homes who are left out of the equation. Freeman's character had legal options available to assist children in even worse circumstances. His abuse of power/corrupt actions undermined faith in law enforcement and harmed the greater community.
So, to recap: 1) He could have saved children in greater need of saving; 2) There's almost no risk of blowback since it would be perfectly legal (unlike this scheme, which always had the potential of unraveling).
Now, one could argue that for Affleck's character this is all a sort of sunk cost. He has to make a decision *at this point in time,* that is, *after* Freeman's suboptimal, immoral decision. However, by siding with the law, he discourages anyone inclined to miscalculate along Freeman's lines.