I don't think the IDF has any credibility. Even if their story is true, military censorship, their history of humanitarian violations, and holding the civilians undermines their position to the point of making it unbelievable.
I also find their excuse for boarding ships in international waters as unacceptable as the US's imaginary war on terror that's used to justify every stupid thing we have done with our military in recent years. They won't let pipes and cement into Gaza because they're at war with Hamas and construction materials can be used to build bunkers! They're at war with Hamas so they can board ships in international waters! They can take prisoners off of boats flying under a Turkish flag in international waters because they're at war with Hamas!
Bullshit.
And ultimately, regardless of the truth of this incident, Israel has put itself into a horrible position over the past three years by creating a humanitarian disaster in Gaza as retaliation against Hamas. This decision to drop commandos on to the boat is a disaster beyond whatever happened - they've created new friction with Turkey and Egypt has opened the border to Gaza. And more boats are on the way to run the blockade, so there's going to be fresh confrontation.