I was recently annoyed to learn that there is no tenant wide way to disable POP3 or IMAP in Exchange Online. Luckily PowerShell makes this task quite simple. This article discusses the various commands that are available, but essentially you'll need to connect to Exchange Online via PowerShell and then run:
Get-User
-ResultSize Unlimited | Set-CasMailbox -PopEnabled $false -ImapEnabled $false
Unfortunately you'll have to remember to disable these protocols for every new mailbox that is provisioned. This can also be performed from the ECP in the Mailbox Features.
