Failure to acknowledge that conservative groups have been improperly targeted for closer scrutiny is not itself perjury.
Indeed, the fact that we're talking about a matter of opinion makes it even more difficult to prove that it's perjury. Also, from what I've read groups were flagged by a set of key words that included "tea party," "patriot", "9/12 project". It's arguable whether or not the motive was to flag conservative groups or to flag groups that might reasonably be trying to wrongfully get status as a "social welfare" organization when they are in fact primarily a political group and should be a 527 groups.
There may well have been wrongdoing in the IRS (especially, as I've noted, if they continued using these flags after it became apparent that they were not productive in identifying problematic applications). But reasonable minds can disagree over that point, and it's not perjury to disagree over what is or is not proper.
So unless someone has evidence that Miller was involved in wrongdoing or intentionally covering up wrongdoing, he should not have been pressured to resign. As Mooseman noted on page 1, the correct sequence of events should have been investigate, verify, then (depending on the outcome of the investigation) terminate (and possibly prosecute).