you can do something on these lines. This code seem to generate valid .zip file in the temp folder.
var zip = new JSZip();
var storage = Windows.Storage;
storage.StorageFile.getFileFromApplicationUriAsync(new Windows.Foundation.Uri('ms-appx:///images/logo.png')).then(function ongetfile(file)
{
var blob = MSApp.createFileFromStorageFile(file);
var url = URL.createObjectURL(blob, { oneTimeOnly: true });
return WinJS.xhr({ url: url, responseType: 'arraybuffer' });
}).then(function onreadbuffer(req)
{
var b = req.response;
zip.file('logo.png', b);
return storage.ApplicationData.current.temporaryFolder.createFileAsync('a.zip', storage.CreationCollisionOption.replaceExisting);
}).then(function onnewfile(out)
{
var content = zip.generate({ type: 'uint8array' });
return storage.FileIO.writeBytesAsync(out, content);
}).then(null, function onerror(error)
{
// TODO: error handling
});