Inasmuch as atomic theory makes use of materials and phenomena presently at hand it is indeed making use of direct observation.
Eyewitness testimony is by no means infallible, but it sure beats none at all. A 4.5 billion year old earth does not enjoy as much, and as such it not a factor in science, but a factor in a philosophy certain folks choose to follow.
Too bad. So sad. Take your philosphy down the hall and preach it.
If you are stipulating that direct observation is dependent on current rather than past observations and this definition is a replacement for the observation of the cause rather than the consequence, you are playing fast and loose with definitions, there-bye making them useless.
The ToE uses materials and phenomena presently at hand, including populations of wild organisms, domesticated organisms and DNA from both extant and extinct organisms.