This is life. We should do our best to be right even though we are probably not. It's that or throw our hands up and quit trying.
Totally agreed that societal mores change over time and you can retroactively realize that something wasn't OK.
The guilt, along with his confrontation with the other Nexuses and the (ambiguous) realization he's the one doing the dangerous work because he too is not a person, is what changes him.