This is a problem with the source format. Epub is inherently an HTML based format, and if the HTML says do-not-reformat that is exactly what the epub is meant to do.
The right way to handle this is probably not to use <pre> tags, but instead use <p> tags associated with a css style that is defined to give you the behavior that you want to see. Unfortunately doing this will require manual work - calibre cannot do it automatically.