Israel never told Egypt to close the border, on contrary, Israel would be happy if all suplies to Gaza were passing through Egypt.
And Gaza is really flooded with medicines, problem that many medicines are outdated or useless. In Edogan's ship some 70% of medicines were expired.
It's more of a give and take. I believe Israel shared intelligence with their Egyptian counterparts with Muslim Brotherhood, which Mobarek and high top doesn't want them to exist.
Also, there is a clear psychological warfare going on from Israel to the media about the flotilla raid. It wasn't Erdogan's ship or anything. It may have supported under the table, but you have no clear evidence supporting that. Also, medicine that IHH tried to deliver to Gaza, could still be usable even 70% of the medice expired, which I can hardly believe due to old anti-trust to IDF.
Perhaps we are missing the point here. Israel is never ever gonna be welcomed in the region until a two state solution established. Just because Turkey decided to foresee new paths to boost its economic diversity, instead of smoothing relations with her, Israel decided to create a new media hype about axis of Turkey, Iran and Syria. In the long run, you can never know US is gonna be a superpower as its current power. When its not, as all superpowers doomed to be shaded into history book pages, you would be on your own with all your neighbours hate you and destroy your state. Can you find a one state in ME that advocates Israel's reason to exist other than Turkey, even today? I don't think you can. Erdogan came into power with democracy and he will go with it.
Look, what Turkey trying to establish in the region with its zero-problem policy. She is not naive to accept it can be peaceful with your all neighbours, but she tries to dim where there is a problem before. After all, Israelis live in the region, not US. Diaspora of Jewish ethnicities in US won't be a lot of help when you don't have a clear agenda of how you wanna exist as a state, other than you just want to exist. When you don't have an agenda of your own other than military power supported or not, you may not have a bright future according to previous historical lessons.