R’ Elchanan opens his Kuntres Divrei Sofrim with the Rambam Mamrim 4:3 –
וכן אם חלק עליהם בגזירה מן הגזירות שגזרו בדבר שיש בשגגתו חטאת ובזדונו כרת, כגון שהתיר החמץ יום ארבעה עשר בשעה שישית, או אסרו בהניה בשעה חמישית--הרי זה חייב מיתה; וכן כל כיוצא בזה
A zakein mamrei is a person who challenges Bais Din’s authority by disagreeing with a ruling of Beis Din relating to an issur kareis, or with gezeirah derabbanan that was instituted as an extension of an issur kareis. The Rambam’s example: challenging the gezeriah derabbanan against eating chameitz during the sixth hour of the day on Erev Pesach (the issur d’orasya takes effect after the end of the sixth hour).
How is this issur derabbanan of chameitz associated with a punishment of kareis? The Kesef Mishne explains that were a man to be mekadesh a woman during the sixth hour with chameitz, whether or not that chameitz is assur b’hana’ah m'derabbanan will effect whether the marriage is valid, which in turn effects whether a breach of that relationship is adultery (=chiyuv kareis) or not.
R’ Elchanan proposes a simpler reading of the Rambam (which I think is the one we intuitively arrive at without the KS”M): since the Biblical issur of chameitz is an issur kareis, the issur derabbanan of chameitz is categorically within the realm of issues one can become a zakein mamrei for objecting to.
There is a something to be said for the KS”M’s interpretation, but before we get to that, let’s sum up the nekudas hamachlokes, the point of disagreement: according to KS”M, it is the fact that chameitz derabbanan can lead to an actual chovas hagavra of kareis which is crucial; according to R’ Elchanan, it is the fact that the the lav of chameitz is categorically subject to kareis which is crucial, irrespective (in this case) of whether there is any actual kareis ramification for violating the derabbanan in question.