I would first ask myself why I *want* a footer at the bottom when the virtual keypad is open.
You have minimal screen real-estate when the keyboard is open. I wouldn't waste it on a footer.
This will be difficult, because mobile browsers try to center the current field in the minimal available space. You will be fighting the browser. I've fought that battle, and it is epic!
I've managed to wrest control from the browser and make the virtual keyboard play nice with iScroll by writing a Rhodes native extension.
But I wouldn't tempt fate by also trying to maintain a footer with the virtual keyboard present!
(Actually, I think it would work, but, then, I get back to the "why" question...)
I think you need to take control of the browser's scrolling of the underlying view. That needs a native extension, and has to be written for each platform (iOS, Android, etc.) Though this is a bigger problem for iOS I think.