"I found it quite cumbersome to read"
The nuances of the grammar make it pretty clear that English is not the native language. Go easy on Babaroga.
"If the protagonist is disobedient and already a rule-breaker, where is the inner conflict?"
If this guy is in trouble for disobeying a direct order, then there is plenty of inner conflict as he struggles with whether to break another rule (and lose his job) or not based on a suspicion he has. Usually, in these types of stories, the protagonist has nothing more than a hunch about a "hellish plan" and faces charges of disobedient behavior if he investigates further and he can't convince anyone else of what is at stake.
"It would be stronger if it were an obedient character who has to break some of those rules to save the day."
True, but an obedient character wouldn't struggle to convince his boss that there is a problem. The interpersonal conflict is gone.