Well I can agree with that. In theory saying terrorists aren’t real Muslims is plainly a no-true-Scotsman thing, as a few of them are plainly part of the diverse part of humanity that identifies as Islamic, and there is hardly a good arbiter of who truly counts.
But you know, the presidential administration doesn’t have the luxury of speaking in the abstract like that; what they say, and the subtext of what they say, are things that have real impact on real people. This is plainly the objection. The only reason anyone might care whether Obama specifies terrorism as Islamic is because they would like to reinforce a link between the two. That gets other terrorism, like the common right-wing Christian terrorism, neglected and gets other Muslims marginalized. You need only look at the results of Trump and his team talking it up.
So at worst this is a lies-to-children kind of thing, a technical wrong for very good reason. Here the administration is trying to deflect real bigotry against real people. Yes, this may make them less popular among bigots who want to see those people marginalized, as the Republicans have been rallying. But if they think that percentage point isn’t worth throwing that minority under the bus, I don’t see why you should fault them for it.