Yes, in a Watsonian sense the Doctor was obviously referring to the other Claras. But in a Doylist sense I did take it as a reference to what Martha went through and perhaps as a reassurance to viewers that Clara was not going to be his Amy-rebound. And of course it also established that this Clara is not the same character as, or at least not identical to, the previous ones. But why would someone have a problem with any of that?