Your etymology is correct, but that has no bearing on the fact that the word has multiple distinct meanings, which is very typical of English. It actually has at least three:

(1) A small number of things (roughly 2)

(2) Two people in some sort of relationship

(3) to join or connect (two) things together

Even though each is obviously derived from the fact that two things are involved, that wouldn't even cross the mind of a native speaker hearing the word in different contexts and assuming the right meaning.