Here's an example of the potential consequences.
T100: Spy swaps civics in your empire, 5 turn wait imposed before you can do anything.
T101: Can't switch back, 4 turns to go
T102: Can't switch back, 3 turns to go
T103: Can't switch back, 2 turns to go
T104: Can't switch back, 1 turn to go
T105: You switch to your original civics, 5 turn wait supposedly imposed. Later that turn, a spy swaps your civics, ignoring the 5 turn wait. New 5 turn wait imposed.
T106: Can't switch back, 4 turns to go
T107: Can't switch back, 3 turns to go
T108: Can't switch back, 2 turns to go
T109: Can't switch back, 1 turn to go
T110: You switch back. Later that turn, a spy swaps your civics, ignoring the 5 turn wait. New 5 turn wait imposed.
...and so on and so forth. It can potentially go on like that indefinitely, as long as there is a minion nation around willing to build a couple of Spies and spend a turn or two on full espionage every now and then to screw with you. There is no minimum wait period for these missions - Spies can enact them at any time... only just switched or not, Anarchy or not.
This is not a "tactic" nor a "strategy" - it's a broken exploit in its present form, plain and simple. It's only made worse in high-level multiplayer games with a large number of human opponents. It's no different than grabbing extra techs with the Oracle or Liberalism - sure the game allows you to do it in regular play, but that doesn't mean it's not highly exploitative. And that is why it's silly not to ban the civic/religion swap missions.
It's foolish to allow exploitative mechanics in a game like this. I would hope that we would all be here to try to test our collective skill and wit across an epic game of Civ4... not to test who can abuse a demonstrably broken mechanic the most effectively.