We do it differently for different Presidents. I mean we had George Bush, but then in 2001 we had to use George H.W. Bush and George W. Bush to differentiate between the two. And for most of the early Presidents we don't use their middle names for. Off the top of my head, I believe the first one is John Quincy Adams, but that's to differentiate between him and his father John Adams.
I would say to use whichever Obama uses to sign bills into law. It's as good as a rule of thumb as any.
And if conservatives want to use Barack Hussein Obama in textbooks, then so be it. It might actually inspire some American Muslim who grows up reading it to actually campaign and possibly win a Presidential election.