Goodness, I hadn't really thought that through. Maybe that's why the scandal was made public and they forced him to resign. He was under considerable pressure from citizens to do something about the charges against Tiller, and he caved in to the Culture of Life with a compromise indictment. Not the worst charges, but still charges.
That means he's got to go, so Sebelius can replace him with a more reliable Minister of Death.
On the other hand, filing charges and not having them thrown out of court is more than Phill was able to achieve. If memory serves conviction on all counts could result in about 20 years in jail and $30,000 in fines. What difference does it make what he's convicted of if the goal is to put an end to Tiller and his business?