I find that difficult to believe. Are you sure both are set not to download your mail, and are instead looking at your mail on the e-mail server on the Internet ?
If you delete on the server no device looking there will be able to see it any more. The iPad wouldn't be deleting it from the laptop but from your server account, and afterwards nothing can find it because the only copy has been deleted.
I suggest using an e-mail client to download to your laptop first then using the iPad simply to view the server account. Then the laptop always has it's copy.