Hi Whitehill, the problem with rules is:
they only work on messages the computer has downloaded.
So, you could leave your computer on and have it check email automatically every single minute, so it's not likely that one won't be downloaded to the ipad and deleted before you get a chance to d/l it to the desktop.
Also, if you have the account type setup as IMAP not POP on the desktop then set=up on the ipad go to "Settings > Mail > Select the account > select account again > select Advanced > then under "Mailbox Behaviors" make sure it says "Deleted Mailbox = Trash" then this way when you rwife deletes a message on the ipad, you can at least browse in the trash folder for that account on the desktop and make sure it was nothing you needed, unfortunately i don't see a rule to act on the trash folder... b/c then you could mark it somehow else.