Unless Hernandez is injured, there was no reason for him not to pitch the sixth. First, it would be one less inning for the bullpen and Garate would likely come in further down the batting order, rather than facing the top of their lineup. It doesn't matter how many more runs Hernandez gave up. The team is highly unlikely to score 6 more runs than the Marlins from this point on, so from that perspective, this game is over.
Riggleman's decision making is highly questionable.