Bovington Tank Museum

Museum opens at 10am, so you could take a train to the nearest station, Wool, and taxi from there to Museum. For example, it appears there is a train leaving Weymouth at 09.20, gets to Wool at 9.45, then taxi to museum about 6 mins drive. Return trip, there is a train at 14.36 gets you to Weymouth at around 15.00 so you will be in good time to get back to the ship if it leaves at 17.00 (5.00 pm). If you choose this option make sure you arrange for the taxi to pick you up at the Museum by about 14.00 (2.00 pm). Doing this you would get about 4 hours at museum.

A quick Google search gave a couple of local tours that included the Jurassic Coast as well as the Museum, possibly similar to the cruise excursion. They seemed to be for groups of 10 and expensive.

The above is all well and good and fine in theory except that you don't dock at Weymouth, you dock at Portland. You are then dependent on a free shuttle bus out of port as you can't walk out, so add the wait line for the bus then a taxi from the shuttle bus drop off point on the Isle of Portland to/from Weymouth station.
The bus also stops at Spring Road, Weymouth, which is not convenient for the station. Then whatever the all aboard time is, and what happens if that train is late.
This is a recipe for disaster.

They often take off ship's tour guests first in such circumstances.
I strongly encourage independent exploration, and avoiding ship's tours. But this is a step too far, (literally in terms of distance). It is unlikely you will catch that 9am train, and the one back is way too tight IMO.
Please take the ship's tour.

I very much understand your frustration, for I have visited the Bovington Tank Museum and rate it very, very highly. I think you can see alot in 2 hours if you study the museum’s website in advance, prioritize what era of tanks you want to see, and carefully monitor your time.