In my opinion, inducing amnesia and paralysis then committing rape is morally wrong because rape is non-consensual and morally wrong, ipso facto. It is doubly wrong if they did not consent to the amnesia and paralysis. Neither does amnesia nullify the physical harm done to the victim - rupturing of the hymen, conception, any bruises or physiological response despite the paralysis.
Regarding trauma and the theory of the mind, if the drug effectively blocks the formation of new memories then we need not worry about any mental trauma from the non-existent memories. There may be indirect trauma when the victim comes to and freaks out due to the unexpected blackout, and any effects.
I am generally OK with medical procedures because these are done with the consent of the patient. If consent is not available then we run into some morally grey situations, and doctors need to be careful to act in good faith.
~Max