Several problems.
1) A Section 31 show would bore an audience, due to week after week of basically the same storyline; an agent of 31 must break the Prime Directive/any other regulation in order to save the Federation. This would lead to unpopularity, and the show would be taken off the air.
2) The violations of regulations would, more often then not, involve immoral actions, leaving an audience slightly disturbed.
3) Section 31 is just dumb.
4) A new Trek show would have to be about a new crew roaming the galaxy, exploring and discovering, not about a bunch of immoral bastards violating regulations.....
I think it's a great idea, a change of direction, we've already had four 'traditional' trek exploring type series, so why not? DS9 was a change from the norm and for me is the best Trek series of them all, it managed to paint a broad canvas of different civilizations and their politics whilst being generally confined to the station, it was excellent. I think just having a crew on a ship going to a different planet every week has gotten tired, and is what effectively killed Trek on the small screen, a new slant is what's needed for me, so I'm all for a section 31 series, it could be awesome...