There's no replacement refs to blame for the poor officiating in the Steelers-Giants game.
Ryan Clark was flagged for unnecessary roughness on a big hit that seemed clean according to NFL rules. Eli Manning threw an ill-advised pass directly at a Steelers' defender, which was followed up by Clark lighting up Giants receiver Victor Cruz. Clark didn't aim for Cruz's head, and the hit came after the Steelers had touched the ball, so there was no question of pass interference either.
Cruz stayed down after the hit, so this may have been a case of the refs calling a flag because of how severe the play looked rather than whether it actually broke any NFL rules. Clark has certainly earned his reputation as a head hunter, but this play looked clean.
You can decide for yourself whether the hit was clean or not by watching the animation below.