increase database size on ipad
This warning is there to prevent people from over filling their devices with local data and also to keep developers in check from not over stuffing the content that gets stored locally.

I don't think there is a way to white list one site to have increased space. I would clear thing by first quitting Safari using multitasking controls, and then go to the settings app -> Safari -> Advanced -> Website Data and clear all the data.

That would allow it to start cleanly. You also might want to be sure your device itself wasn't totally full by checking Usage under general in the settings app.