It makes one wonder whether, with Section 31 gone, the Federation might suddenly find itself on much dicier ground.....
Just because their methods are distasteful doesn't mean they weren't effective!
Then it's up to the Federation to make
Starfleet Intelligence that effective - and, unlike S31, do it within the bounds of the law. Don't tell me they can't do it, either. There's nothing S31 can do illegally that SI can't do legally. And if there is, it shouldn't ever happen in the first place.