There are two ways of looking at this: first, that the Israeli police are one of the most corrupt and repressive among countries calling themselves democracies. Rape, abuse of power, corruption, theft and all sorts of similar charges are made and substantiated regularly. Another police commander was accused of raping the director of an Israeli NGO in 2009 and admitted to inappropriate sexual contact. So the fact that a senior officer is accused of rape is entirely credible.
Rape and sexual harassment seem to be perquisites of office for many male Israeli officials. The list of those alleged, charged or convicted is long including Moshe Katsav, Haim Ramon, Yitzhak Mordechai, and Gideon Saar. The mayor of Kiryat Malachi recently joined the ranks of this august group.
Among his other claims to fame, Shaham commands two other notorious abusers abundantly profiled here: Meir Rotter, who enjoys beating Sheikh Jarrah activists; and Doron Zahavi (aka Captain George) accused rapist of Mustafa Dirani.
Shaham voiced harsh statements about the Gaza settlers who were evacuated by police in 2005 (though no less harsh than police statements about peace activists). His appointment to his current position was vehemently opposed by the settler right. So it’s possible that this charge is politically motivated.
UPDATE: There are those out there who ferret out any possible misstatements or errors published and get their jollies by pointing them out and passing them on to pro-Israel shills like David Lange or David Abitbol. Haaretz’s confirmation of my reporting will leave them mute once again. Haaretz finally reported this story (including the charge of rape) once that gag was lifted. We had no such constraint. I hope the gag was lifted at least in part because I was able to break it.