My best advice for avoiding paint rub is to avoid painting joints. Seriously, whenever possible I try to choose a lighter colored extremity, and use RIT dye for synthetics to bring the color to what I need. Not as big of a challenge as one might think, as there are a lot of browns and blacks in Star Wars costumes, as well as creams and beiges to start from. If the color is close, often dry brushing doesn't rub nearly as bad as a solid coat. I have heard others have good luck with spray vinyl detailing dyes, but I haven't tried this yet.
If you do have to paint joints, you're pretty much stuck using your dremel. If at all possible, I try to avoid extreme color shifts (black or dark grey to white, for example), as the remaining disc edges of the ball joint still tend to stick out. One thing you can try, after carefully sanding and painting , is applying a very thin coat of Superglue with a toothpick to protect static surfaces. Be forewarned, however, that if it oozes next to the disc, it is difficult to impossible to free up that joint safely.