Apps that only show up in iCloud (under your purchased apps) can not be deleted, because they are not really there. The App Store keeps a list of all apps you've ever purchased, so you can download them again free, if you like. That is what shows up in the App Store under Purchased. They take up none of your iCloud storage spaced. This is true of all your iStore purchased content.
Apps can be hidden from your Purchased list using iTunes on a computer, but I don't know of any way to do this from the iPad. Hidden apps are not deleted, and can un-hiddnen by going to your Apple ID account settings, again in iTunes on a computer.
Now, if you're talking about your iCloud backup file, the app should be removed from the list of backed up apps as soon as you do a new backup. If not, you can delete the old backup and create a new one manually. These options can be found under Settings > iCloud > Storage & Backup > Mange Storage, then choose your device.