Wow! Sounds like you definitely ran into problems with that one! Sorry it didn't meet with your expectations. Mother Nature just did not want to treat you well. I agree that HAL should have provided a bit more for your troubles to help ease the pain.
By contrast, we did a 14-day cruisetour with HAL (3 nights on the Zaandam and the 11 nights inland) and it couldn't have been better. We also lucked out and only had one day with some drizzle - unfortunately, that was the day we went on a tour into Denali park, so we didn't get to see Mt. McKinley. But HAL treated us wonderfully and we would do it again.
I feel bad for the problems you encountered - everyone should be treated to a nice Alaskan cruise.