The easy answer could be to either rank the disciplines in order of power (semi subjective) or perhaps put them into three tiers of power (a little less subjective), and allow a trade for another discipline of equal or lower power. Thus, you could trade Iron Heart for Shadow Hand if you really wanted, but not the other way around.
If the person wanted, perhaps you'd let them trade
two weaker disciplines for a higher level one. This would be a boon two sword sages who get six disciplines, three or four of which are pretty crappy. They could keep Diamond Mind and Tiger Claw and trade for any two of Devoted Spirit, White Raven, or Iron Heart. Of course, at that point, they might as well play a warblade for the better chassis and recovery method!