I would probably do it, just for the different views. Getting close to the icebergs and seals is something I really wished I could have done last time. (In 2014 they didn't have the small boat excursion, but there were other small boats in Tracy Arm, and I was really envious of the views I was sure they were getting. I'm taking the excursion this summer.)
One thing to consider, since the excursion is one-way, you'll also have one way on the ship. The decks are crowded on the way in, but once they've seen the glacier, most people go inside. So if you do the early excursion you can have the small boat going in, and the decks of the ship to yourself on the way out.