The only way to accomplish this is to use a scheduled script on the channel to make sure the file exists with the header.
Here is the script to remove any header rows from the message before writing it to the file.
var rowContent = message.getNode('*[1]');
message = qie.createCSVMessage();
message.setNode('/', rowContent);
Here is a sample scheduled script to create the file with headers.
qie.moveFile('c:\\temp\\csvHeaderTest.csv', 'c:\\temp\\csvHeaderTest' + qie.formatDate('yyyyMMddhhmmss') + '.csv', false);
qie.writeFile('c:\\temp\\csvHeaderTest.csv', 'Header1,Header2,Header3,Header4,Header5\n', false);