^Yeah, but abusive parents "don't mean to" hurt their kids either, or at least they don't think they do. Some people love, but love badly or corruptedly. I mean, come on, realistically, anyone in that room could've been hurt or killed by shrapnel from the explosion, regardless of their position. (Hell, realistically, the overpressure shock of the blast in that enclosed space could've killed everyone in the room and the hallway.) It's an insanely reckless thing to do, using explosives to blow open a door that your own son is on the other side of. Manta may love his son, but he's still a bad guy, and that excess aggression in pursuit of his goals and failure to consider the harm his actions can cause are part and parcel of what make him evil.
I think your usage of the word 'realistically' gave me pause. This is a cartoon about super powered teens or young adults, so I don't think we can judge it by 'realistic' standards. I think Manta's actions fit with his character as depicted on the show thus far and that's fine with me. Manta's action was reckless, but he's a bad guy as you pointed out, so his disregard for the lives of others and his single-minded focus to reach his son despite the damage that might cause works for his character and makes sense in that regard. I could also see Manta being arrogant enough to believe that his eye beams were precise enough not to cause any collateral damage that would concern him or hurt his son.