As Ben pointed out, you can use RestraintSets to weight things. This does get to a more fundamental problem that weighting inhomogeneous restraints relative to one another is fundamentally broken and should be avoided. We are working on solutions to that (using an inference based optimizer Keren developed), but for now you have to fool around with weights.
Just to be 100% sure to understand : what you mean when saying this approach is "broken" is that rather a technical / software problem, it is a fundamental / theoretical evilness / badness to mix "things" that do not leave in the same space. Though, since a more theoretically justified technique is not yet at hand, a weighted sum of restraints will do the trick.
Concerning Keren's development, has it got anything to do with Domino ?
In addition, if you use Conjugate Gradients, the derivatives of the excluded volume score on atoms are pretty useless since they are computed using each atom ball (explanation of the problem would probably benefit from a picture, I'll work on that :-).
I tried with a picture, but couldn't make anything that wasn't confusingly cluttered.
To try to explain better, for a pair of intersecting rigid bodies, the derivatives of the excluded volume restraint are computed by adding up the derivatives for each of the balls which constitute the rigid body. The sum of these individual derivatives does not necessarily point in a direction which separates the two rigid bodies unless the inter-penetration of bodies is small compared to the size of the balls. As a result CG would get stuck in local minima.