You know we're ignoring a few potential key factors if I'm not mistaken, here's my take:
1. Dad
While I believe the Dad knows SOMETHING about the MC's Mom's death, I think it's obviously related to some form of monster attack. But I believe with confidence that he had NO knowledge of the college's special situation. I know everyone loves to huff theory copium on the forum here that every little detail means something bigger but sometimes it's just simple (no offense). So let's establish the facts;
-Dad works in part with the government and does shady shit on the side, definitely has connections with non government as well no doubt.
-Disappears for crazy amounts of time without knowing what he actually does.
-Lives in a disheveled apartment.
-Deep rooted alcoholic, disheveled, and quirky all the time, could barely sneak up on his rival detective.
-Sent the MC to a school filled with H.E.R.O connections and soon to be superhumans alike.
From all of those out of the way, I'd wager he's not James fucking Bond, knowing about H.E.R.O, monster armada attacks, the works, ain't no fucking way on god's green earth. This is a man who witness his wife die potentially from a monster, was kept silent and offered a job by the government somewhere regarding that field but not by any big capacity, and disregarded. Now the college can be explained by the simple fact that; this is THE primary sector. PM lives here, top of the Mafia, richest man alive, etc. OF COURSE some shady connected guy is going to use his connections to put his son in the best college, not involve in the same world that potentially killed his mother. Ain't no way he knows any of the crazy shit, hell even the PM wasn't aware of what was REALLY going on.
2. Deus
This could be completely wrong but if I'm not mistaken Deus said he was an acquaintance of hers? This entire point could be nothing but I didn't see anyone bring it up if it was true. We know Deus sees whatever bits of the future, and that he has a keen interest in us, and our development (based on his interaction with Valravn), sound familiar?
-What if this Ella isn't the original, and the original died when Christine mentioned she had, "changed". It would explain how Ella grew SOOOO fast despite not having the resources like H.E.R.O AND being relatively the same age as the MC upon receiving her powers. Just throwing it out there.
3. Knowing
So the Ella is Ella bro. I know I ride her dick hard but fuck it, let's do this. She has honest moments with the MC. It would be ridiculously stupid to put on a whole act with music changes and everything, going into a band, whatever, just to be like, "HA just kidding! I killed your Mom!" Referring to the MC by first name might be explained by her doing research ahead of time on them for compatibility with the pills, or if it ties into my Deus theory.
That's my take, I'm tired so take it with a grain of salt. Moral of the story is the Dad is not this all seeing eye, Ella has a LOT of secrets, but our relationship with her (compassionate side) is genuine. And she is by no means the cause of our Mom's death (though she may not the reason behind it through whispers or events who knows).