Personally, I think it was the emotional intensity and need of the Doctor for Clara that was erased. If it was a "simple" memory erase, there would be a thread and he would go "pulling on it".
If it was just his memory of Clara that had been erased, just how long do you think it would it take for him to notice there are holes in his memory? Not long. And the one thing the Doctor can't resist is a mystery. Therefore, it can't be a straightforward memory removal.