Stop access to the iCloud notes app on a lost iPad, but keep my notes on the iCloud website?
Did you enabled the 'Find my iPad' option on your lost device? If so, you can go to iCloud.com and remotely delete all data on the iPad without losing your notes in iCloud. 
If not, did you use a passcode? All data on the iPad is encrypted and it is highly unlikely that someone evil finds your (locked) device and tries to hack into your notes.

Another workaround would require you to use the Notes application on an OS X computer. Set up your iCloud device and another email account that supports notes (most IMAP accounts do). Then open the Notes application and move all of your notes to the new account. This will eventually sync with your lost device, but you would have to access your notes in the new account.

I do not think that there is a perfect answer to your problem, everything left to do is some damage control.