So, I have this big encounter set up. It's got everything; there's monsters and traps and a big set-piece battle to bust into an enemy fortress! The players are all ready to go, and then the warlock says those dreaded words....
"I'm gonna use Diplomacy."
Oh god. He's level five, and he rolls a total of 32 (18 on the die + 4 charisma + 5 trained + 5 power bonus), so now I have to deal with it.
Diplomacy isn't "I make them do whatever I want if I roll high enough." It can influence an NPC only if that NPC is willing to be influenced in the first place and won't force an NPC to do something against their nature, like violate their orders or make them take their own life.
On the other hand, if you want to con a group of guards that you really are authorized to pass the gate and your letter from their commander got burned up in a battle with a hydra, Bluff is the skill to use. I'd probably give a 10 or 15 point penalty for a bluff that outrageous, but a lucky player specialized in Bluff might pull it off.
And don't get too wrapped up in the "Encounter Power" cost, it's going to get used in just about every conversation you ever have with that player until the campaign ends since he can use it every 5 minutes.
In the future, if you end up with a set piece like that, make sure the players are going to fight before you spend any time setting up your maps and minis. Also, accept that the players are going to end up going over, around, through or under some of your prize encounters; it's what they do, encourage them to succeed in unexpected ways and reward them for doing so. If it happens, let it go, and file your set piece in a "to be used later" folder. A couple of months down the line you can reuse the encounter with some higher level monsters and a bit of tweaking so it looks like a completely different encounter.
The one thing you don't want to do is continually override the player's ability to defeat challenges in nonstandard ways. One of the most annoying things a DM can do to his players is make their choices and plans meaningless by visibly forcing them on a set path through an adventure.
The key is visibly, there are lots of things you can do behind the scenes to get things back on track and it's usually not too hard to drop in an extra "wandering" encounter to make up for one the party breezed through with luck or a good plan. Also, keep your calm and if you are unsure of your ability to improvise on the spot don't be afraid to say "Wow guys, I didn't see that coming." and either end the session early or let everyone take a break while you shuffle things around.