I am a huge Casualty fan (no idea why, I just love it). I think they usually have quite a progressive, up to date view of issues.
However, I totally agree with you OP. I just couldn't get my head around the message in the story line that you are referring to.
They seemed to imply that the 'holy grail' for children where parents have separated is to be adopted by a step parent. That, as you say OP, this will make them a proper family.
WTF! It was a terrible message to give out. It was made worse by the fact that the boy's father clearly loved him a great deal and there was scope for their relationship to get closer. But oh no, father realises how dearly he loves his son, and decides he will sign the adoption papers.