Charybdis is a whirlpool, an act of nature that would not have been defeatable. Scylla, begin a living monster could be killed under the right circumstances. While both were deadly, chances are with the other living being. If enough men were able to shoot arrows, or if they were likely to catch Scylla asleep, then safe passage would have been possible next to Scylla.
It turns out for Odysseus and his men they made the wise choice. If they would have gone towards the whirlpool, loss of life would have been total loss. However, because they went toward Scylla, they only lost six men to her appetite.
With Scylla They were Gaurenteed to lose at most six men with Charybdis they would have all been killed regardless