Right. You have to look at it in context. Ordinarily, if Qui-Gon had been trying to just buy something for personal gain, yes, that would have been a dark act. But in the grand scheme of things, it would have made things much simpler in obtaining a hyperdrive in order to get the Queen to Coruscant in order to try to find a way to end the siege on Naboo.
However, despite that example, there are some inconsistencies between the movies, games, books, etc. However, with the NJO, you have to remember that Luke had very little guidance on how to rebuild the Jedi Order, hence there are going to be some dissimilarities between the "policies" of the old and new Jedi Orders.