I'm surprised you didn't get an e-mail from Juneau Car Rental back in March when they changed the policy. Perhaps it went to your spam mailbox? Juneau Car Rental just sent me another e-mail yesterday, inquiring about how many people I have in my party so that they can coordinate shuttle pickup. Did you get such an e-mail? If not, maybe it's because you already told them group of 7 back in February, so they already have the information? At any rate, this is just further confirmation that rental car pickup at the dock is no longer available, and yeah, super frustrating.
My big problem is our ship doesn't arrive in Juneau until 2:00 PM. With them saying that it could take up to two hours for shuttle pickup, it could realistically be 5:00 before we're in the car. And to compound that, their shuttle only runs until 8:00. They do offer the option to drop the car off after-hours, but then we'd have to find/pay our own way from their main office back to the ship. I think I'll end up cancelling my rental reservation with them.