One way I can see to avoid that is a convention where outputs are always a standard size (integer powers of two, for example).
I like this idea, although enforcing it network-wide might have other implications (or maybe not, I'm not sure). A script could be written to easily condense a users outputs prior to a CJ tx, so gmaxwell's original design can be followed:
To use this to increase privacy, the N users would agree on a uniform output size and provide inputs amounting to at least that size.
I think Peter Todd wrote something that cleans out dust, you could just rework that to accomplish the above methinks.
