calibre and Sigil both have the ability to regenerate the Cover page, and will wrap the cover image in an SVG. As you have seen, there is a good reason for that.
The SVG wrapper should declare the true size of the image, and it will be
scaled appropriately. That's how both calibre and Sigil generate them.
If you are adding SVG wrappers, you can do it all right then and there.
calibre's Modify EPUB plugin should allow you to recreate the cover (using proper SVG wrappers) in all your EPUBs in bulk -- without changing anything else, like conversions would do.