Yes, the clitoris was always part of female anatomy. All mammal species have females with clitorises, and apparently ostriches have them too, and a few other species as well. This shows that the evolution if the clitoris happened WAY before the first humanoid creature emerged.
What cataclysm? Mitochondrial Eve is just the earliest common ancestor of all now living people. In all other aspects, she was just like all the other women around her. Women back then probably looked a lot different than women do today, but their clitorises was probably one of the least different-looking aspects.
The clitoris is a female aspect. That's why it's present in the fetal stage where we are all female. Our nipples also come from that stage. The clitoris is the primary anatomical source of human female sexual pleasure. There is nothing degenerative with it, quite the opposite; without it, there would be much fewer human beings. (Oh, wait; you might have a point after all...)
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It can't be removed, as most of it is under the skin. The glans (head) of the phallus is reminiscent of the glans of the clitoris. Your fore-mothers and current mothers sought/seek to remove it because they want their daughters to be married and the troglodyte men in these cultures seems scared of marry a woman with a sex-life.
There is no valid reasons for female genital mutilation. There is only one valid reason for male genital mutilation; if the prepuce is too tight.
Women also have prepuces. Neither men nor women ought to be mutilated before they are adult and can decide for themselves.
