Here's a scenario to illustrate their positions and why MC follows Draxus even though he has higher position than Draxus does. Think MC as young crown prince and Draxus as his teacher, yes the crown prince has higher authority and position, but usually accepts the teacher's position, since the teacher is still more experienced and is teaching the young prince. It's pretty much the same situation in here, MC accepts that Draxus has way more experience and knowledge than he currently has, so he accepts Draxus as his teacher and thus accepts the authority of Draxus in these situations. Same with rest of the people there, they know that Draxus has most experience to take on the temporary leadership position and train MC to be what he is meant to be.
Also to your other point about the girls not being there when MC's parents died, it is explained in the game, that MC's parents were in undercover operation at the time, with Draxus and the rest being hunted by the gods and Dagon's cult, so it's not like they can keep tap on what is going on MC's life all the moments, not to mention that them coming to MC might have even put him in more danger than let him "disappear" in the system so to speak. Also the fact that the Norns appear to kill MC is extremely drastic action, it's not like they can take matters into their own hand too much, gods are not omnipotent and omniscient in this setting. The fact that they took the risk they took, by altering the timeline so drastically is already something they could get into trouble.
