I think those anomalies are fine, If anything I like them like that. No choice involved. It just goes with the concept that sometimes you cannot control everything and the best part are the funny stories
The problem lies in that you are forced to unlock the first perk once you have 20 pts.
This could be an issue if, for example, you wanted to be good, but you get 20 malevolent points by accident. You are forced to unlock malevolent 1, which makes Benevolent 1 cost more.
If you could choose to use or not your ethic points, there would be no issue.