Sure Emily has made mistakes, she was young, stupid and pregnant. She was no doubt desperate and Andres jumped in there, somewhat to get back at Santiago as he hated him. Their relationship was never going to last, given how it started.
Andres should never have asked for the MC to never be told the truth, that wasn't his decision to make. Everyone should know where they really come from. Emily should also have never agreed to that, but we all make mistakes.
Personally I find it more upsetting that the MC missed out on his Mom for five years, I know that it was necessary for the plot but still, you only have one Mom even if she isn't as perfect as many would like.