I believe that the notation AC first appears in Cook's "A Taxonomy of Problems with Fast Parallel Algorithms" from 1985. On page 11 (page 12 of the journal) we read:
To state a more general form of this result we introduce the following terminology.
Definition. $AC^k$, for $k=1,2,\ldots$, is the class of problems solvable by an ATM in space $O(\log n)$ and alternation depth $O(\log^k n)$.
This class is actually a uniform version of AC.
There follows an alternative characterization by Ruzzo and Tompa, appearing in a technical report by Stockmeyer and Vishkin, and later on in "Constant depth reducibility" by Chandra, Stockmeyer and Vishkin from 1984. They use the notation SIZE-DEPTH(poly, constant) (see page 3).
Cook goes on to mention another unpublished characterization by himself and Ruzzo. Further results due to Ruzzo are mentioned, including $AC^k \subseteq NC^{k+1}$ ("On uniform circuit complexity", Ruzzo, 1981). The latter paper (as well as Ruzzo's earlier paper also mentioned) doesn't contain the notation AC, but rather a myriad of other notations, emphasizing the notion of uniformity used.
All these papers mention alternating Turing machines a lot, giving credence to the hypothesis that A stands for alternating.