That wasn't the only criticism of Cruikshank in Heller.
The Heller decision cites with approval a new book (2008 anyways) by Charles Lane titled "The Day Freedom Died". "The day" in question was the day Cruikshank was handed down by the US Supremes in 1876.
Cruikshank set the stage for thousands of lynchings by claiming that the worst possible civil rights violations by states could not be controlled by the Feds, ending reconstruction. In the events that led up to Cruikshank, white cops and other town authorities stripped arms from blacks for the specific purpose of launching what turned out to be three days of arson, riot, rape and murder. The "heinous crime" the blacks had committed was attempting to vote under the new 15th Amendment.
Cruikshank is the most screwed-up precedent imaginable and I think the cat is way out of the bag and running off down the street about how foul it is.