Either reduce the ship or module transfer times outright or offer expedited service at a premium. Having your ship or module sent where you want it doesn't put another player at a disadvantage and....
Nah,
The ability to instantly/cheaply transfer ships certainly DOES give those with sufficient credits an advantage because it means they can travel in a ship optimised for travel and then instantly switch to a ship suitable for trading/mining/shooting/whatever with no planning, forethought or compromise required.
Course, I'm sure somebody will immediately be thinking "well, everybody's got heaps of credits now so that doesn't matter" but I'm afraid that's just something else that's broken and it's not smart to screw something up just because a different thing is already screwed up.
Personally, I'd say the cost of ship transfers need INCREASING to suit the current level of available income.