When the DM has to start coming up with ways to modify encounters in order to deal with his party, that's a sign he's actually tailoring his adventures to the players, and that their characters actually matter to his game world, and it allows the players to still use their fun abilities without you having to cry 'It's broken, waaaaa' and hit it with the nerf stick.
There's two schools of thought on this. Mine, personally, is that abilities that seem strong have weaknesses, and making encounters where said weaknesses are exploited are fair game. By the same token, making encounters where said strong powers 'save the day' for the party is also fair game. The idea of this is to create experiences and good adventuring times, not to perfectly balance the system out as tho it were some competitive MMO.
The system as you run it only needs to be balanced between the players actually playing, and the monsters they come up against. Anything else is superfluous.