Review and deploy the VipsScaler extension on Wikimedia so that large PNGs can be properly scaled. The VipsScaler supports conditional scaling, so it is possible to configure it to scale only images that match a certain condition (i.e. area > 12.5M)
Such a condition would look like:
$wgVipsConditions = array( 'mimeType' => 'image/png', 'minArea' => 12.5e6 );
Note that a the development version 7.25 needs to be installed on the image scalers because older versions do not handle certain PNGs properly.
Unfortunately there are a lot of dependent phase3 revisions in BitmapHandler, so this can probably not be done until deployment of 1.18.