Yes, this is basically my view as well. If I have to pick one of these two, I go with the SL6 option (but I think both have merit). And yes -- as few stops as possible after the bridge, assuming that SL6 is implemented without removing buses from the 104/109 (i.e. riders heading for Sullivan still maintain as much access as today). The only exception I would toss out there would be a stop at Bunker Hill Community College -- not the train station, just near the intersection with Austin St. That seems like it could be a potential destination unto itself, so worth considering. But I don't think other stops along Rutherford are necessary, and my gut says that a diversion to Sullivan is not worth it.
To be clear, my support for the Rutherford route is contingent on it being a speedy route -- I assume that would require bus lanes, but perhaps traffic moves quickly enough that they are unnecessary (I am skeptical, but). And I think the offering is significantly stronger with a BRT extension to South Station, although I think a Haymarket terminus would be perfectly reasonable in the short-term.
Running via Rutherford is not about serving Charlestown -- as you say, already served by the 92. It's about providing Everett a direct connection to downtown -- Everett being one of three municipalities directly bordering Boston that does not have such a connection (once GLX finishes), and by far the closest and probably the most transit-oriented of the three. (The other two are Winthrop and Milton, the latter possibly being debatable.) Rutherford just happens to be the best (only) road connection between Everett and Downtown, but conceptually it's no different than the Haymarket North extension running through/by Charlestown without really serving it, or a hypothetical Green Line branch to Chelsea doing the same.
As for Sullivan-Lechmere-Kendall: I think that needs to be a separate service. As of now, there are no plans for bus lanes in Cambridge between Kendall and Lechmere (as far as I know), so reliability will be significantly reduced. I think that calls for a shorter service. Also, as mentioned above, a Sullivan-Lechmere bus route could tag along with an Everett-Haymarket route by leveraging bus lanes on Rutherford to the Gilmore Bridge (which I believe is a slightly shorter route than going via McGrath).