Strange that the "Processing" layer isn't preventing the additional click.  Just to verify... you set the Form properties to show the processing message... correct?

Have you tried to add the "Ask Confirmation" option to the button, this might help to inform the user that the button was clicked the first time. This is under the functionality tab under behavior.

Is there some event that is triggered after the form validation that I could wire into, to disable the link button at that time? If the network connection is slow, or the server is slow, the user has pleanty of time to click the link again.

Is there anything that would prevent the processing message from showing? 

We have found that if your workflow form is inside a web part for example on Sharepoint, the processing message was not showing.  I don't think we have figured out what the conflict is.

You could possibly have another form when the user hits submit telling them a summary or a message letting them know everything went through.

your form is long, the processing message won't grey out the entire page.  It still allows you to click submit and it does not have the option to be on the bottom of the page, just the tops and center.
I think this is a bug...

I noticed that too. Only greys out the top 3/4 of a form in 1280x1024 resolution for me.

I"ve confirmed the Processing message not covering the entire page is a bug in 6.5.  It has been fixed in the upcoming version 7 release.