It's not a "missing fundamental option". If you have 'Leave messages on server' checked that is exactly how it should behave. Deleting emails on the N900 should not delete them on the server so they can be downloaded to a pc later. That's how I handle all my email. I don't want my only 'master' copies of emails to be on my phone.

What it seems you want is for each time you delete an email, for a option box to pop up with the choice to delete only from the phone or the phone and the server. That is really not possible with pop3 email.