Peterhansel won 6 Dakar events on a motorcycle in the 90's, he's well versed in racing both cars and bikes. That "hit" was merely a nudge at idling speed while crossing a quickly flowing, and deep, river. It could have been a poor calculation of where his fender ended, a result of water unweighting the car and forcing him down stream a bit, or trying to make the exit point without hitting the bank. I guarantee it wasn't a purposeful act.
I've met the man...he's a compassionate person. Whether it was his idea, or that of the ASO, an apology seems like the proper conclusion to an unfortunate situation.
I agree with Tim, it's not safe for bikes and four wheeled vehicles to race together. Unfortunately it's an inherent risk you assume when competing in an event like this one.