In the past, I have read that if you give your passport to Guest Services, they can get it stamped for you.
We were able to get our passport stamped last year b/c we actually went through customs at the airport in Vancouver before getting on the cruise. We never went anywhere else that it was stamped on the Alaskan cruise. Even though in Skagway we did do the white pass railway and went into Canada, they just looked at it and let us through.