Yes, the Queen took the throne at the twilight of the British Empire. But it was in the midst of the Malayan emergency, the Mau Mau uprising, the Suez crisis was on the horizon, and South Africa had just launched the apartheid regime. Those were all, in different ways, attempts to stamp out democratic independence. Britain didn't relinquish its sub-Saharan African and Caribbean territories until the 1960s. You cannot cleanly separate the Queen from the empire which she crowned.
I think you're choosing to couple the British monarchy with the Empire.
The Queen willingly became head of a Commonwealth that included dependent colonies, and a British state that was actively repressing several independence movements. That the head of the Commonwealth is coupled with it is obvious, not my 'choice'.