With what was known about Centaurs, most likely. They may have not done this often, but since Umbridge used magic against them, it is most likely the case. It is not clearly implied that she was raped (it is more implied that they had roughed her up a bit). However, Starkid may have understood what that implied since they openly said in AVPS (a very potter sequel) that Umbridge and the centaurs had coitus (Firenze's word). However, they also implied that the coitus was consensual, since Umbridge and Firenze were seen together looking like a couple at the end of the musical.
However, it can also be implied that Umbridge wasn't raped since she may have used her influence at the ministry to kill every centaur in the forbidden forest. Since the centaurs were still in the forest at the end of the seventh book, openly fighting against the Death Eaters, it is possible that she didn't do anything about it or that she was too scared to have them removed from the forest. Hermione most likely didn't know the Centaur myth or didn't realize that they were angry enough to go to that level in torturing Umbridge. Also, when she returned in the seventh book, she was torturing muggleborns, not trying to get revenge on centaurs.
However, as horrible a woman, human being, and witch as Umbridge is, no one deserves to get raped.