At end game you basically have two choice raids/dailies and pvp. I personally think you've underestimated how demanding pvp players are, and as a whole, how much of an impact pvp would make to your game. Having said that, by simply putting a stop to further exploitation is not going to be enough to fix the issue. The large valor gains players have received are going to unbalance the entire games pvp element more so than it already is. In essence the pvp portion of the game will still be hemorrhaging from this if you dont roll back valor experience. I like this game a lot but the pvp element is killing it for me. Ilum as a whole has been bugged from the moment I got there. All Ilum provided is a breeding ground for exploits, from credits to ill-gotten valor xp.
No one should blame you for taking back what players illegally received through exploitation. They exploited the game, and nullified the agreement. Take it back. However Im sure this option has not escaped your notice which leads me to believe you may be incapable of rolling back valor xp. If that is the case you are going to have to consider a more drastic measure.
BW you are new to MMO's, thats ok, we all make mistakes. Where your strength will come from is how you respond and fix these errors. MMO players are the most fickle and the most demanding because we are paying a monthly subscription. You made a mistake, now you need to fix it properly. Just remember what happened to AoC, learn from that. Good luck.