I still feel like it's the kind of double life that anyone associated with the justice system would frown upon. One of the safeguards of the criminal justice system is that the different levels of jurisdiction are compartmentalized. The police might work in conjunction with the DA, but ultimately, the enforcement/investigation, prosecution/defense, and judgment operate in independent jurisdiction with independent rules. As far as "only protecting the innocent", well, a defense lawyer's job is to defend his client to the best of his ability, regardless of their guilt or innocence. Sure, you can pick your clients, but I'd have to wonder exactly how partial Murdoch would be if he discovered his client was really guilty of the horrendous crime he was accused of.
I'd personally love to see Matt Murdoch hang up the mask for an extended period of time. Give us a book about Matt Murdoch, defense attorney, focusing on his cases and the various components in his firm. Step away from the suffocating broodiness that have haunted the past two and a half decades of the character's existence and give us a procedural set in Marvel's New York City. Gotham Central from the perspective of the court system.