If that's the case I'd expect them to deal Rupp. Bring up Knapp and let him play 3-4 times a week with a supplement of Ellis 2-3 times. Knapp learns on the job while being an apprentice to Ellis. Young pitchers get to work with Ellis a couple times a month. Alfaro gets a full season at AAA.
We already know they don't think Knapp is ready and want to pair Rupp with a veteran back-up. The problem is Knapp is on the 40 and wouldn't get to play a lot in AAA. But if they don't like Knapp as Rupp's back-up they probably don't like him more as the almost-starter (and Ellis shouldn't catch 80-90 games either).
I imagine there is still a good chance Knapp is traded, but they can also find the 40 space eventually. Rupp could be traded in July or next off-season. I don't think they will trade Rupp unless they are ready to have Alfaro in the majors (though you could also make the case to just do that now).