They were assigned other duties.

Depending on how you interpret the word "repercussions" that would mean the answer is yes - their chances for promotion might be jeopardised or in the worst case scenario they might be demoted; or no - they were neither incarcerated nor executed. You would think that refusing an order in wartime would at least lead to a court martial, and this was frequently used as a defense argument in war crimes trials, but in effect there are no records of anybody ever being tried for refusing to kill a Jewish person. It was tacitly recognised that this was an extraordinary and unusual situation. Otto Ohlendorf, head of Einsatzgruppe D (one of the special units tasked with the mass murder of Jews in the Soviet Union), admitted during the Nuremberg Einsatzgruppen Trial that he had excused from duty men who could no longer cope with the stress of the executions. He even admitted that he himself could have refused the command of the Einsatzgruppe.

Source: Trials of War Criminals Before the Nuernberg Military Tribunals Under Control Council Law No. 10., Vol. 4: United States of America vs. Otto Ohlendorf, et. al. US Government Printing Office, District of Columbia 1950.

Likewise, the men of Reserve Police Batallion 101, tasked with executions of Jews in Poland, testified in Christopher Browning's Ordinary Men that they were given the choice of withdrawing before and even during the executions. Some would simply slip away and hide until the "action" was over, without any repercussions. Between 10 and 20 percent did so.