As I understand it, "ɑ" is the original form, as the letter arose from the lowercase alpha in the Greek alphabet. When did the modern print "a" appear, and why is it almost universally used in print when "ɑ" is still typically used in handwriting?
Actually, both double-story and single-story lowercases are found in printed typefaces.
Historically, the divergence arose in the 15th century Italy, when two forms of scripts arose, which are stilled used today--roman (upright) and italic (slanted). The first roman typeface was developed by Nicolas Jenson, which was based on Roman majuscules (hence the name) and Carolingian minuscules, a form of calligraphy ultimately derived from Roman cursive. The first italic typeface was Aldine, named after the printing press where it was invented. Its founder Aldus Manutius created it to squeeze more information into a smaller number of pages:
“We have printed, and are now publishing, the Satires of Juvenal and Persius in a very small format, so that they may more conveniently be held in the hand and learned by heart (not to speak of being read) by everyone"
The reason it has the single-story "ɑ" is because, as you said, because it was on the humanist cursive in vogue at the time, which did emulate the Greek form.
Of course, this is no longer the case. While we still have roman/book and italic formats for typefaces, designers mix and match features for many reasons. The reason you probably see a two-story "a" on your screen right now is because your default display font is probably set to either Arial or Times New Roman. However, you can change it to one that uses a single-story "a", such as Futura.
tl;dr: Change your font if you want the "ɑ".
EDIT: Department of Redundancy Department.