While I understand the security concerns I'm not sure if the raid was executed as well as it could have been. I wasn't there and don't know exactly how it played out but I'm not so sure that it was the best move at the time. It could be a tough call though.
The Israeli raid on the Gaza flotilla was not a strategic move, and instead could have had severe consequences for Israel. The purpose of the flotilla was to provide humanitarian relief and comfort. While, there might have been political motive for the flotilla, there is substantial evidence to proof humanitarian efforts were the main cause of the flotilla. If Israel had any suspicions, they should have used legal action through diplomacy, instead of violence and force. The unprovoked attack, thus, cuased the deaths of numerous people, and questioned the ability for Israel to achieve peace.