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The sequence number is the sequence number of published messages. You are not supposed to change that or set that yourself as then you could only do it exactly as is or wrong (according to what it is supposed to be). This is why you can't change it nicely.
Your fix just tells ROS that there is no place (header) to store the sequence number and thus it can't supply one. If you need some unique number in your custom message, you should just define another message field.
I can't really see a use case, where you'd need to set a user-defined sequence number in an sensor_msgs/Image message that is used by a standard ROS program.
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