Characters act very human in this VN, they aren't perfect and they make mistakes, usually out of very relatable motivations. Emily probably didn't think she would lose her son for 5 years when she sent him to stay with his step dad, she's also(imo) the instigator of her divorce which was a great contribution to those 5 years., and she clearly regrets this decision and having wasted all this time.If I remember correctly he was sent away because he had become very angry and unruly and his mother could not control him to the pont that he was becoming abusive towards her and others? He's grown up a bit now even though he still has some way to go (imo). But great VN, one of my top 3.
Still, on most cases it's up to the player wether it's in you to forgive these mistakes and start fresh or you want to have a cold relationship with the women who "wronged" you.
Ps: I'm always surprised on the visceral reactions to Emily given that she's not a love interest, i thought those kinds of reactions would be reserved to those cans of worms (they also make their fair share of mistakes), she's your family and until she does something truly unforgivable it would be the best to support each other... and it's obvious that even with the mistakes she might've made she's trying her best.