Footage from the Mavi Marmara's security cameras:
It's possible the activists weren't trying to create the kind of violence which broke out. But it is looking less and less likely that the IDF initiated a violent incident aboard the ship.
It seems pretty clear by this point that the operation was under-resourced and quickly got out of hand. But that in and of itself is enough of a mistake to cost Israel a victory. Israel's mistake started before the operation even began. It's important to keep in mind that the failure here was not tactical but strategic.
That being said, the IDF press office is doing a pretty good job at what it's supposed to do. The narrative from Israel has been clear, concise, and generally supported by video footage. Considering the circumstances the press office finds itself in, it's hard to think of more they could be doing in the current political situation.