My 2 cents, Emily is a good mom, she means well... but she wasn't a good wife.
Since the MC is the son, i think he should be in good terms with his mother... But from an outside perspective i can see why Andres thinks she's a bitch.
When she agreed to marry Andres and make him the father she agreed to keep Santi out of the family, when she starts meeting Santi she is betraying that promise.
Yes, the "letter" of the promise is never tell the MC he has another father, the subtext is "the 3 of us is the family, no one else gets in, specially Santhiago".
I also don't get the continued meetings, sure you ran into him once and decided to tell "the baby is alive and well and he considers Andres his father, he has no idea about you", but why the continued meetings? Are you gonna keep updating him about how the kids doing in school? Wether he gets a girlfriend or not?
Again, if you have an agreement he can't interfere, it doesn't make much sense... Makes it seem to me that although she didn't go forward with it, she was at least contemplating jumping ships.