First option: Get rid of IE.
Safest work-around I know.
More seriously, you can disable MSE by opening it, going to the Settings tab select 'Real Time Protection', and uncheck the 'Turn on Real Time Protection' box.
If you already have Flash Player installed, it should update itself, without having to go to the download page. You can make Flash Player check for updates itself by opening it in your Control Panel. The update check is in the 'Advanced' tab. It brought me to Adobe's site, which may still cause an issue for you, but I was already fully updated, so give that a try too.
I'm running MSE and can get to the page and do a download without a problem. Have you tried navigating there starting from just the basic
www.adobe.com ? Then hit downloads, then select Flash Player.