That in itself doesn't necessarily mean ill intent. Someone who knows what to go after can be very useful, if they chose to utilize that knowledge.
Also, the IRS is big, the commissioner does not decide cases, however it issues policy memos, which have a large influence on enforcement. And these are usually public and or can be FOIA-ed.
So all in all, their pick is very much a political ally, and that he/she happens to be a tax specialist is just a convenient factor. (So that the man is fit to deal with IRS stuff.)