Do I Corrupt or Destroy?

In ending my work in progress, I have reached a point where I have to make a decision.  Is it better for an organization to be corrupt and the main characters to take moral offense and leave the organization?  Or is it better to just wipe the organization off the face of the planet?  Should I corrupt them or destroy them?
The Benefits of Corruption:
  • I have weighed this carefully and I have decided on the following reasons why corruption would work in my episodes:
  • The main characters would have a valid reason to leave the organization
  • The main characters taking moral offense to the practices of the organization adds to their character and gives them a certain depth and helps define what they consider right and wrong and how they respond to good and evil
  • A corrupt organization offers the possibility that, like the mob, once you’re in you can never really get out so the characters will have a constant foe or a foe that can be brought in and out of the story conveniently when needed
  • A corrupt organization offers an unlimited supply of new characters that can be introduced at any time in the future
Now, on the other hand, the following are the benefits to simply destroying the organization with some outside attack:
Benefits of Total Annihilation
  • The organization would no longer exist
  • The destruction of the organization would offer a common bond between the main characters due to their shared loss
  • There would be no wrapping up any connections to the organization, no problems with character interactions, no explanations
  • It frees the plot for other good or bad guys to enter
  • It can be a really cool way to introduce a new bad guy by their destroying the good, noble organization
So there it is, laid out plain and simple.  So which do I use?  I think the answer lies in whether or not I need to lean on the organization as an evil entity in future story lines (I am working on a series of episodes for a show so each episode has its own story).  Do I need a source for future bad guys or would I rather be free of the burden of continuing the story of the organization?
Which do you prefer as a reader?  Do you like large corrupt organizations in the background?  Do you like the consistency of the characters always fighting against the same overall enemy?  Or do you prefer variance and unpredictable bad guys?

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