I figured out what the problem was about. I assumed jpg php functions could not handle the transparency, so i removed those lines and forgot about them. Apparently it just creates a white background and it does not fail. So the script is as follows:
$filename = dirname(__FILE__)."/uploads/" . $_FILES['myFile']['name'];
$filename = str_replace('.jpg', '_retina.jpg', $filename);
file_put_contents($filename, file_get_contents($_FILES['myFile']['tmp_name']));
$image_info = getimagesize($filename);
$image = imagecreatefromjpeg($filename);
$width = imagesx($image);
$height = imagesy($image);
$new_width = $width/2.0;
$new_height = $height/2.0;
$new_image = imagecreatetruecolor($new_width, $new_height);
imagealphablending($new_image, false);
imagesavealpha($new_image, true);
$color = imagecolortransparent($new_image, imagecolorallocatealpha($new_image, 0, 0, 0, 127));
imagefill($new_image, 0, 0, $color);
imagecopyresampled($new_image, $image, 0, 0, 0, 0, $new_width, $new_height, $width, $height);
$new_filename = str_replace('_retina.jpg', '.jpg', $filename);
imagejpeg($new_image, $new_filename);