Yep, precisely. And it would give context to some stories as well. For instance, no way in heck should a Sith Warrior should be taking orders from Darth Marr - not in the context of the story. He answers to a "higher power". However, if there was a class story attached, where the Hands told you Marr was coming and had an assignment on Makeb for you to complete while there, AND make it look like you are getting along with Marr per orders... suddenly the whole thing takes on a new context.
Personally, I think they can always use Makeb as an experiment with the idea first. Its already there - why not add some class stories there? Would make a good testing ground to evaluate risk and check sales - its short enough too so any quest chains wouldn't be too lengthy.
It is too late for Makeb to be fixed, that ship has sailed already. Your idea could work for another planet though although it would be a bit of a pain for them as they would have to finally get round to acknowledging all of the possible endings for the various classes. Yes most of them only have 1 real ending but Agent has several, some of which got totally ignored in the opening cut-scene for RotHC.