I think it's possible to concede that in some way, Muslims do indeed worship the One True God, even if they badly misunderstand him and man's relationship to him.
It goes without saying that the revelation of Christian Scripture and the Qu'ran cannot be reconciled. They can't both be right. The Qu'ran denies that Christ is God and denies the Resurrection. Jesus is reduced merely to a very great prophet.
For all that, the president's words, however well intended, go overboard. It's possible to show respect for Muslim beliefs - nay, even to admire some facets of their faith (most Westerners could learn from their intense devotion to prayer, for example) - without giving away the theological ranch.
Why doesn't he go to the Church of Satan then? They also have beliefs in a Diety.