Actually, a LOT of CRs 2 over the characters will still chop them in two. The power of gestalt PCs is more in versatility than direct power. More foes is usually the better idea, especially mooks to mop up on [while the mooks are actually sweeping away those oh so precious actions]. Keep the CRs themselves closer to normal unless the players are milking gestalt, but increase overall encounter levels.
And double check with the players to see if they might like slower advancment. It is VERY easy to level too quickly in gestalt. The Power level of gestalt characters can quickly leave the comfort zone of some players and DMs. For some there is that "sweet spot" that once the game is in, the player needs time to learn how to use and enjoy their new abilities, rather than mull over the strategies needed once they again level up and have to deal with justifiably stronger foes.