My dear friend, the Mirrer Ilui, R' Tzvi Moshe Kantor answered this kashya with the following illuminating distinction: A regular לאו הניתק לעשה is composed of an aviera with a cheftza and a mitzva with a cheftza. For example: He stole the object and now he performs the mitzva of returning it. He fixed the aveira - so no malkos. Teshuva, however, is on the gavra, he is fixing himself but the aveira on the cheftza is not rectified. Hence, the malkos remains in force.
Gevaldik.