Although there is some interest in 'following the money' and nailing corrupt politicians etc they are not 'the target' or any kind of priority for the detail. Its not just a case of the 'Barksdale Crew' getting more lenient sentences - if the detail were to turn the case over to the FBI it is more than likely that the original targets would be offered immunity by the US Attorney for turning Statesgiving evidence against corrupt officials. The detail are not as interested in corruption at this stage as they are in getting the murderers they have been chasing the entire season. Seeing them walk scot-free just so the FBI can make high profile prosecutions on the back of their work and personal sacrifices (from what I remember Greggs is still gravely ill at this stage) really does not seem appealing to any of them at this point.
With respect to the 'Brass' continuously shutting down investigations that may compromise them, this kind of goes right to the theme of the show. The city is peppered with corruption top to bottom. In one instance, Burrell and Davis plan to present information regarding illegal activities from Daniels' past, showing that they are united with regards to their entrenchment in this institution (and that, as an aside, even Daniels is hardly squeaky clean himself). When things begin to fall apart amongst them, Davis berates his black colleagues in positions of influence for 'not being on the team'. Aside from that the managers know that Freamon and McNulty are the worst fire starters in the department and are continuously wary of them sticking there noses in any direction, given that once they start pulling on any particular loose thread the whole house of cards may come tumbling down. There is clearly a 'good old boys club' entrenched in Baltimore that do not feel that they are answerable to anyone.