There is actually a good earlier train combination - 5:23 from Munich Hbf (2 hours earlier than your plan) with the same one change 300 metre walk between the two stations at Frankfurt airport, getting you in 2 hours earlier at 10:20, if that would help.
Early breakfast though.... or take it with you on the train and enjoy at leisure.
No the boats are not "hop on and hop off" but you could get off one and on the next if you pay and plan that way.
For me, I'd take the boat downstream (south to north) and then back by train. The slow train goes past the same castles and valley, next to the river, and the view is of the same stuff just a fair bit more quickly.
To go one way by boat and then back by another boat would be a bit too slow for me and a bit repetitive. The view on the boat is all-around, and the boat goes slowly enough to see everything from all angles. If even that is too fast for you so you want to go back for more, just take the upstream boat, north to south, which because of the current goes even slower than the downstream boat and may give you enough so that you are happy going back by train.....
