Why are they requiring a Civil Engineer, who is likely an exempt employee, to actively log his hours, then fire him over that specific reason? That company is in danger of making ALL civil engineers non-exempt, and be on the hook for overtime for the past two years on every single one. Sure, he could be fired for pulling that crap, but it should have been phrased differently, mainly involving his availability for projects.
I'm in the camp of "It doesn't matter, as long as you get your work done," however, it depends on the job. Sometimes you HAVE to be in the office during normal business hours for impromptu meetings, phone calls, etc.