The power of the Rabonnon

The gemara in Shabbos on daf 14 - 15 talks about different levels of tuma that the Rabonon placed on various things. I can understand them saying that the things should be nitle (safek tuma) but how could you be soreif truma or kodshim on a sofek or because of a gezeira? There's an isur d'oraysa (at least an isur asay) to be meabed kodshim or truma b'yadayim because the pasuk says mishmeres trumosai. So how could the Rabonon override that with a kum v'asay of destroying it?