I am saying it may even be beneficial. I've made this point perviously but I will run it by you again. If the Juniper is more foliage dependent for the support of the tree reducing down the foliage is going to create an imbalance in that the roots are going to be calling for nutrients from foliage no longer available. If the roots are reduced then you reduce the demand on the top of the tree.
In this case, where the top has been so drastically reduced, reducing the roots may be the only way of saving the tree. The idea that "gee, I have all these roots supporting just this little bit of foliage, that's got to be good." It doesn't work that way, the mass of roots will continue to demand resources from a top that is no longer there and the top that remains will be sucked dry by this activity. This is what I believe and this is what history in my experience has shown.
I plan on mixing my soil, root pruning, and repotting today.
-Mike