It's just that way with advice... you now have 3 different plans from 3 different posters.
We all agree on this for a trip to Eltz:
"...do the river cruise FIRST on the way to Eltz. Then stop at any of the towns on the train ride back if I still have time. "
I am on the same page with Jo on this:
"If you only ride the ship between Bacharach and St. Goar you will have missed a major part of the beautiful scenery and lots of castles." It takes just 40 boat minutes to enjoy the Bingen-Bacharach segment as well (otherwise you can try to catch a few blurred images from the train window - the train trip takes about 10 minutes.)
But I would not board in Rüdesheim for 2 reasons. 1.) The extra 15 minutes on the boat do not offer additional sightseeing since that time is spent crossing the river to Bingen only. 2.) The hourly trains that get you to R'heim arrive inconveniently in Rüdesheim at :04 minutes after the hour (if they are on time.) The KD boats depart at :15 after - this isn't an adequate window to get off the train, get yourself to the KD dock, buy a ticket and board. This would mean leaving Frankfurt at 6:53 a.m., arriving in R'heim at 8:04, then waiting an hour for your 9:15 boat departure. IF YOU BOARD IN BINGEN you get to have breakfast... you leave Frankfurt at 7:47 and arrive (after one change of train in Mainz) at the Bingen Rhein Stadt train station at 8:59 - which leaves you 31 minutes until your 9:30 boat leaves the dock.
Whether you take the train from Frankfurt to Rüdesheim at 6:53 or to Bingen at 7:53, the cruise boat will not be any faster, and you won't get to Eltz any earlier.
Boppard, St. Goar, and Braubach are all great places to visit and you could have a great day without going to Eltz. But with your tight day and your goal of visiting Eltz, I side with Lee on getting off in St. Goar. You've cruised the best part - now get yourself to Eltz ASAP. You will have about 30 minutes in St. Goar for a quick look around and maybe a snack. Board the next train and you should be in Moselkern just before 13:00. Do you have this walking guide to Eltz?