It must be remembered that the information that the newspaper gets is second hand and therefore often incorrect. I have read numberous articles about the Kirksville execution from around the country in the days that followed and few get the number correct (Even some Union reports have the number wrong.) The location of Macon was incorrectly stated in the article as someone confused the follow up skirmishes in Macon County a couple of days after Kirksville and assumed the executions happened at Macon.

According to the Missouri Republican (St Louis) on August 14, 1862:
"After the defeat of the rebels [at Kirksville], some fifty persons, who had heretofore been paroled or taken the oath, were shot down."

On August 16, 1862, the Burlington Hawkeye (Iowa) also reported fifty shot down.

Given enough time and no other news, I'm sure it would have got up into the hundreds.