True; and the Doctor exists as an idea (even when he's "officially dead" later on, too). Maybe there is some link with Time Lords "in many ways, having the same mind" as per the Master/Doctor link, and the TL's on Gallifrey having a link even through their time-bubble to The Master (and he to the Doctor, and the Doctor to River, etc, not to mention Romana in E-Space perhaps!) so it's impossible to erase every vestige of them from the universe. There are even the communications-cubes in House's blister-universe, which operate telepathically. So if Amy reboots the entire universe from an idea/memory, maybe River was the memory of a memory (being her daughter, perhaps a fairly strong subconscious one)... or something. A lot less to animate than a universe, anyway.
If the ruddy Daleks can survive annihilation in Time Wars over and over again then the Doctor deserves to