For posterity, here's what I came up with. Seems to work pretty well:

var flaBase = base + "media/flash/assets/accessories";

var allFlas = FLfile.listFolder(flaBase + "/*.fla", "files");

for(var i = 0; i < allFlas.length; i++){

          var flaName = allFlas[i];

          var doc = fl.openDocument(flaBase + "/" + flaName);

          var targetName = doc.name.replace(".fla","");

          var cjsDataKey = "CreateJSToolkit_data";

          //var data = doc.getDataFromDocument(cjsDataKey);

          var data = [

                    "version", "0.1",

                    "exportHTML", "false",

                    "frameBounds", "false",

                    "includeHiddenLayers", "false",

                    "soundsPath", "sounds/",

                    "preview", "false",

                    "imagesPath", "images/",

                    "libraryPath", "libs/",

                    "compactPaths", "false",

                    "exportSounds", "true",

                    "imagesNS", "images",

                    "exportLibs", "true",

                    "libNS", "lib_" + targetName.toLowerCase(),

                    "hostedLibs", "true",

                    "exportImages", "true",

                    "outputPath", "file:///outputpath/",

                    "createjsNS", "createjs"

          ];

          doc.addDataToDocument(cjsDataKey, "string", data.join("\n"));

          doc.save();

          doc.close(false);

          // Re-open document so that Publish for CreateJS panel picks up changes.

          doc = fl.openDocument(flaBase + "/" + flaName);

          fl.runScript(fl.configURI + "Commands/Publish for CreateJS.jsfl");

          // Insert an artificial pause here. Seems to be necessary for Toolkit publish.

          alert("...");

          doc.close(false);

}