I'm sure Israel would turn back most all small boats since terrorist could use that, but if there are small boats arranged to come in by groups along with Israel, then you are all set to go.
I bet that is the way it would go.
One of my colleagues was helping with the French evacuation yesterday. He complained about how many Arabic names were on the manifest and was told that it was too late to vet the passengers. Anyone with a French passport was allowed to board, Hizbollah or not. So this is not just a "small boat" problem. And an understandable sticking point for Israel.