What do I do now that I know my one parakeet is seriously hurting the other one, but they love eachother!?

Rocket and Peanut the parakeets (2 boys) were bought as babies at the pet store at the same time but are not from the same nest. Over the 2 months I've owned them I have lovingly hand trained them to the point where they are super tame. They do everything together, but Rocket is a bully and progressively more and more so. To the point where I found 3 little wounds on poor Peanut where he has been bitten or scratched. The sad thing is these parakeets love each other so much that they cry for each other when they are separated. I have separated them but is this the only way?? Poor Peanut.