I believe that you are on the right track. However, instead of another government institution (which will simply become co-opted in time), the solution would be for your country to bring back private prosecution. Private prosecution is firmly entrenched in English Common Law (upon which the laws of your country are based) and predates the use of Crown Prosecutors prosecuting the majority of cases (instead the Crown Prosecutors only took cases which were of interest to The Crown). Victims (or there friends, relatives, &c) were responsible for the prosecution of the offenders.

While I am not advocating scrapping all public prosecution, in cases where the defendant is either a government employee or strongly tied to the government, there exists an implicit conflict of interest (regardless of the level of awareness that the prosecutor might hold). In addition, the ongoing relationship with the constabulary requires consideration. Virtually every law society precludes its members from engaging in cases wherein a conflict of interest would exist. These rules need to be enforced.

A benefit of this would be to open the field for prosecution of those which are politically connected, or those who commit offences which the administration du jour do not wish to see prosecuted. With this open field, if a group become co-opted, another may simply form (much in the manner in which an open-source project is forked). As a protection against malicious prosecution each prosecution is vetted by a neutral party (the court) prior to commencement.