Don't Fix It

The Gemorah in Sukkah (33b) considers removing berries to make a haddas kosher for use on sukkut מתקן מנא, a toldah of מכה בפטיש.  Most Rishonim (Rashi, Tosfos Shabbos 103a) assume that this rendering a haddas halachikly fit for the mitzvah is a Rabbinic prohibition.  On the other hand, the Mordechai (siman 837) understands it is a Torah prohibition.  The Gemorah in Beitzah (18a) is clear that toiveling a vessel or a person immersing in a mikvah to become pure from tumah is only a rabbinic prohibition.  According to the Mordechai why is it not prohibited according to Torah level?  In addition, Rashi Pesachim says that sprinkling from the chatas on a person to allow them to bring the pesach is a rabbinic prohibition.  According to the Mordechai it should be Torah prohibited?  

I believe there are two approaches to answer the question.  One approach is that the Mordechai only holds its a Torah prohibition when there is a physical change to get it started as in picking off the berries from the hadas.  In the other cases there is no physical change so a halachick change in its own right does not constitute a Torah prohibition.  Another approach is that it is only when the halachik change creates a new חפצא like a hadas that it is a Torah prohibition but when it merely enhances the object or person, making them halchikly pure that is only a rabbinic prohibition.