There's a whole number of really good reasons IE does this, and I'm sure it's not something anyone would argue with - so the main objective is to get around it somehow to make things better for your users.
Sometimes its worth re-thinking how things are done. Perhaps disable the button, use javascript to check when all the fields are filled out, and fire off an ajax request once they are. If the ajax was successful, enable the button. This is but one suggestion, I'm sure there will be more...
Edit: more...
Do simple submission (non-AJAX), and if the checks fail, send a page back rather than an attachment. The page sent back could contain all the information originally submitted (plus whatever error message to the user) so the user doesn't need to fill out the entire form again. And I'm also sure there will be more ideas...
Edit: more...
I'm sure you've seen this type of thing before - and yes, it is an extra click (not ideal, but not hard).... an "if your download fails, click here" -> in this case, do it as you want to do it, but add a new link/button to the page when the AJAX returns, so if the download failed, they can submit the already validated form from a "direct user action". And I'm sure I'll think of more (or someone else will).....