Several points:
I am one of those dinosaurs who happen to agree with 411A on this one.
The controller is not at fault. His responsibility is to scan the rwy prior to or at the same time as issuing the take-off clearance.
All runways that are open are "active". Any one or more of them may or may not be "in use".
Any pilot who insists on "verifying" his clearance to cross any and all runways along his assigned taxi route to his assigned runway may find his flight headed to the "penalty box" at ATL, ORD, or LAX, etc.
With the FAA and FBI redacting the controller's name from the public access reports, Mr. Chicken ***t must feel like a real man revealing his identity.
When the FAA made the rest regs, and Comair applied them to their schedules, I'm sure no one counted on the Captain having his family coming to visit on a 10 hour (legal) layover, especially with 2 small children who are suffering from colds.
Learn from this crew's mistake...don't try to excuse it.