If you are converting the books in Calibre, (epub to epub conversion), look in the Epub Output options, and Uncheck "Preserve Cover Aspect Ratio."
If you want to edit just the cover page *without* converting, open the book in the Editor, Delete everyting between the <body> and </body> place your cursoe between those two tags, click Insert Image Button, Make sure that Full Page Image is checked, and Preserve Aspect Ratio is *not* checked, then click on the cover image.
Unfortunately, I do not know a way to automate this. The Modify Epub plugin has an option to replace the cover, but no options on how it is formated.
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