I came up with a system for signatures on email documents that are used in emergency services. I thought it was trivial. I offered to provide the public key server for the system. I wrote up the step by step procedure to do it. "Copy the message into the clipboard. Use WinPT to sign the clipboard. Enter a passphrase. Paste the signed message back into the editor. Hit 'send'". We aren't doing it because "it's too hard". And guess what? I've come to agree that it is simply too hard for most people to do something even that simple, because it has to do with computers and "computers is hard".
So you're comparing "type email, click send" with "type email, select all, exclude the signature block, cut the message (not copy - or they'll dupe the content), open a new application, click a button, enter the passphrase, switch back to the message, paste in the signed text, click send" and you don't understand why a user might think it's "too hard"?
OK, OK, that's fine. Here's a suggestion. Make it easy for the user and they'll be more likely to do it.
Write an extension to $MUA that puts an extra button in the toolbar for "Sign and Send" (or replace/extend the existing button). Hook Ctrl+S, Ctrl+Enter (or whatever keys $MUA uses to send email). When the message is about to be sent, pop the passphrase dialog up and let the user enter their password (have three buttons: Sign and Send, Send Unsafely and Don't Send).
Yes, you'll have to do more work. You might even have to fire up Visual Studio to do it rather than hacking in vi. But the chances of success will be greatly improved if the user doesn't have half a dozen manual steps to go through. (Thinking about it briefly, you should be smart about the dialog only showing up when messages go to a particular address, or set of addresses, which would also greatly improve usability).