TS3 has always been horribly inconsistent with step-relations and I don't think there's any way to fix that. But sims should not be interacting with and reacting to what the game labels as parents-children and stepparents-stepchildren any differently from each other especially if they are all in the same household.
However, you may wish to use NRaas MasterController to remove the mother-child relationship at some point in the future if you do not wish the stepchild to be passing down genetics from a sim who is not really their biological parent.
