The biggest issue here is post Novus stage the weapons have customised secondaries, how do you decide during the exchange what secondaries are present on the weapons? I would vote that you could exchange the current weapon + fee (gil,quest,MGP,GCP whatever) for a different one with no secondaries thus forcing you to complete the sphere scroll novus phase to customise it. This way it not only gives people the option to swap weapons there is enough of a downside to stop people from abusing it.

You can already buy sphere scrolls and outfit them as you wish for other jobs in advance anyway (AFAIK) so it wouldn't even render you with a disadvantaged weapon if you wished to be prepared.