Thank you for your thoughtful response.
I think your point one is basically a question of definition: what does it mean when you apologize. I think I disagree, but it may be cultural. Should Israel have apologized for the flotilla? Assuming Israel was correct.
Perhaps part of this is that you are saying they should apologize for PR reasons, while posters above were suggesting they should because it is appropriate to.
I’m not sure where you are going with point two. If you mean to state that Judaism was cast in a negative light by this story: I agree. But any more than that, such as ascribing fault, is as you say, incorrect.