The logic of the heter machira as disqualifying the institution of shemitta is in fact impeccable.
Heter machira recognizes the unworkability of the rabbinic design of shemitta, and so proceeds to suspend the institution of shemitta. The Jewish people can thus repudiate the avonot avotam itam through the mechanisms of the avotam itam.
With the heter machira the rabbinic community is in effect saying they can't deal with shemitta – that it's too hard. Rabbinic scholarship is simply not up to the challenge of building the sort of practicable institutional sub-structure that would make shemitta doable so the rabbinic decisors are throwing up their hands and opting out.
That is fine for the Jewish people. Through a simple legalistic contrivance the rabbinic community is taking itself out of the business of administering shemitta and leaving it for other elements in Israeli society to tackle.