Although I have no intention to verify this but it is my belief that you can not change how iOS puts a field navigation bar when the keyboard is displayed in Safari. I tested in a few web apps out there (notably gmail) and it is there as well.
In iOS app development that bar that Safari puts above the keyboard is a view that the application puts there not something the content (your web app) creates or has access to.
Unfortunately the only way I know of is to create your own iOS native app and have it load the web app. (See mailroom app for an example).