An immune system that only kills cells determined to be 'non-self' would be woefully insufficient. It needs to kill cells that have become unhealthy, for instance clogged up with misfolded protein, all the time, even when those cells are clearly still 'self'.

See also my comment to ubernostrum further downthread. There is no compelling reason to frame cancer or infectious disease as a conflict or invasion. Doing so is just as reasonable as framing housekeeping as a conflict with 'foreign dirt' or an invasion of 'the outside world into your house'.