I've spoken to the design team about the issue of Grade 7 ship upgrades and the cost in game (resources and time) versus the cost on the Cartel Market, since this concern was raised by a number of people on our forums.
Our Lead Designer for the game, Damion Schubert, has this to say:
We are currently looking at solutions that cause the least amount of frustration for all players affected, while keeping the integrity of both the Cartel Market and the game intact.
So the solution turned out to be:
"The costs for Grade 7 ship upgrades available from the Fleet vendor, Daily vendor, and Starship Upgrades credit vendor have been reduced." (http://www.swtor.com/patchnotes/1.6.2/182013
So no refund of overspent commendations/credits, then? Needless to say, it's not enough.