The modern day bitcoin trader should carefully consider whether they want to be a part of a market where the largest actors aren't bound by the rules they set for everyone else.
In this case, however, only some parties knew that MtGox's internal accounting was broken. Therefore, the price run up may have been "illegitimate" for a limited time period based on this asymmetry of information.
You are right though that over the long term a market price is always "legitimate" by definition, because of the maxim "something is worth whatever someone is willing to pay for it."