One approach is a more extensive use of tugboats on the open seas. It may be difficult for non-mariners and non-engineers to understand, but ships have a very poor directional control. Most ships are not designed with directional thrusters. Outside of specialized vessels such as oil rigs and tugboats, civilian ocean-going ships cannot "turn on a dime", relatively speaking. They don't need to, either, except when in ports. And there, the tugboats are almost always available to lend a hand.
Therefore, in a protest scenario like the Turkish flotilla this weekend, a tugboat is very useful. By applying leverage at the bow, a tugboat can push a ship in the desired direction, toward an Israeli port instead of a Gaza one, for example. And that's assuming that the boat cannot tie a rope on the ship. Two tugboats, one on each side of the ship, can squeeze the bow and pull the ship in the desired direction, in a limited fashion. In the worst case, the tug can push the ship toward a shoal or bar, running the ship aground and thus immobilizing it. If the shoal is in hostile territory, a marine detachment establishing a bridgehead on land is still much better than commandos securing a ship from hostile protesters.
In a less lethal confrontation as envisioned here, we can expect protesters to impede tug operations by throwing projectiles at the tug. The tug can use its firehoses to limit attacks. In addition, the tug crew can operate under shelter, limiting the effectiveness of non-explosive weapons. The onboard firefighting gear counters the threat of molotove cocktails.
Therefore, in enforcing naval blockades, navies need to include tugboats to provide the maximum range of responses in the OOTW environment.