I've been around ships my entire life. I'm not sure how one "clogs" the fresh water intake of a 2,000 ton ship at sea while underway. Other than a torpedo, the only way to do what you're suggesting - stopping a ship underway - is to disable the rudder. This has inherent risks as a errant shot could easily hit something other than the rudder.
The IDF is between a rock and a hard place. It's tough to stop a ship without some collateral damage, and in this case, that means protesters deaths.