The Earth may (I think it likely) have been tectonically active for long enough to destroy any such traces of an advanced civilization arising during its first couple eons (oldest macro-fossil: 800m years; Earth: 4.5b years).

Better disproof is perhaps the absence of evidence in the geologic/atmospheric record. One imagines that a geologist in the deep future could detect a long-forgotten humanity via the record's abrupt spike in CO2 output, just as present geologists know of the Great Oxidation Event.