I mean, if you want to turn a grey issue into something completely black and white, sure.
If you want to assume that because you got some dirt on your shoes, you should just throw them out. Even if you just had to step out of the way of a runaway car.
We literally know nothing about the relationship between Section 31 and Starfleet from that exchange other than that one is letting the other get away with shit. That absolutely speaks to a level of corruption and probably desperation (based on everything else going on in the quadrant at the time), but it doesn’t speak to a level of involvement of one with the other.
It’s the same as Paradise Lost… does one admiral and their staff attempting a literal coup. Does that mean Starfleet as a whole is condoning that coup? Should we just throw the whole thing out because of that incident?
Sure, if you think any measure of corruption means that it’s not worth supporting something anymore.