I hear that many companies are now adopting a 'model of advocacy' which enables crewmembers to challenge the behaviour of one or more people.
If the crew had said something like "Captain - Why are we flying at this height (pause for explanation) - this is against the rule, please climb to safe altitude" They may not have been disciplined.
Unfortunately, rule-breaking is prevalent in this industry and so many accidents have resulted from a sequence of non-compliances. Why?
What should have happened is the pilot should have his licence suspended.