I've always etched the ITO first and then deposited the aluminum using a mask, so I've never done what you're asking. I think I remember hearing that FTO is much more etch-resistant, but I'm not sure if that would work for you.
You could try masking off the ITO with clear lacquer and then etching the Al as usual with whatever acid you prefer. ITO under the lacquer will survive an acid bath, then you can remove it by sonicating in acetone. However, the ITO immediately under the Al might not take so well to that.
What are you using it for? (Sorry, no one else asks these questions here and I'm excited.)