This is a game, it's supposed to be fun. The players are unhappy about the change, as they were 'optimised' under the previous rules set. You are introducing a new rules set. What possible justification can you supply to not allow the players to optimise their characters, when you will be using the new rules set to optimise the NPC's?
Get the players on board about this. Get them to feel fully involved, and get them to buy in. Tell them that you have heard their concerns and think that it is only fair to allow them a full respecification of their characters. Let the players rebuild their characters from scratch, allow then to change anything about their characters they want.
Statistics, Money, XP, Magic Items, Equipment - all of this stays the same, everything else is up for grabs.
Also tell the players that in 3-5 sessions from now they will be allowed a limited re-tooling in negotiation with you, if they discover that they have made sub-optimal choices.
It's NOT about punnishing the players, it's about having fun in a game.