Like I said its more about the greater good, S31 actions gave the Federation serious leverage on the Dominion and it ended a war which the allies could have ended up losing even with the Cardassian's switching sides.
There is nothing wrong with wanting the world to be squeaky clean, open and above board but its just not a realistic outlook, mistakes will be made and bad things will happen which creates opportunities for good things and vice versa, it will never be as black and white and clear cut as you want it to be.
I especially liked the quote from McCoy that
@Greg Cox posted above "evil tends to triumph over good unless good is very, very careful", I couldn't agree more, in fact living in a world where such organisations exist is a comfort as it shows that the powers that be aren't walking around with their heads up their ass.
With that being said I have no problem whatsoever with Pike not liking it as we saw in the episode, as long as he acknowledges the necessity of it, which he did when the Admiral confronted him about it, I felt it was handled well and also shows that there is some oversight, its just not what we would call official.
I do look forward to finding out who this control is and learning more about Leland and his ship in the new series.