I can't comment on the Tracy Arm Fjord excursion as our visit to TAF was canceled due to ice, but I would jump on it if it was available. I understand they sell out quickly.
As for doing a 2nd excursion same day in Juneau, you would likely have time if you find a late day start, which there usually are. The Mt Roberts Tramway runs all day, so you would be able to go up there and enjoy the view and hiking trails. There are also evening whale watching excursions.
If you can grab a rental for the evening (we've gotten one for earlier in the day & don't know if they're available for later or not) you can venture out on your own - there is a lot to see. The rental pick up is very close to the pier.
Enjoy your cruise!