You can accomplish this using the following code.
// set message to Pipe delimited file (without header row)
message = qie.createCSVMessage(false, '"', '|', '', false);
// or, set message to Pipe delimited file (with header row)
//message = qie.createCSVMessage(false, '"', '|', '', true);
//Convert via a regular expression
message.setNode('/', source.getNode('/').replaceAll('(,)(?=(?:[^"]|"[^"]*")*$)', '|'));