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With Android 4.4 KitKat, Google is upgrading linux kernel to version 3.8 which is the required kernel version for Docker.
I don't know the AUFS part but will there be a way to run docker containers on android with this update?
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It depends if this kernel is compiled with the required features to run containers. If it's the case, then Docker could be used on Android (especially Docker 0.7, which is in release candidate state right now, and doesn't require AUFS anymore).
According to the documentation, the Android kernel is missing quite a few of the kernel features needed by LXC.
Perhaps in the future with Docker 1.x, it might be possible to write a plugin that uses Android features instead of LXC. But for now, you would need to build a custom Android kernel and then build LXC for it.
There are some people actually working on that, and Stéphane Graber has a good summary of the difficulties on his blog.