You can do this by writing a wrapper script that executes the real node with --harmony, then instruct Passenger to use that wrapper script. For example, create /home/user/wrappers/node:
#!/bin/sh
exec /usr/bin/node --harmony "$@"
Then:
chmod +x /home/user/wrappers/node
Passenger Standalone uses the first 'node' command in PATH, so you can do this:
export PATH=/home/user/wrappers:$PATH
cd /your-app
passenger start
If you use Passenger for Apache or Passenger for Nginx, set the appropriate directives:
# Apache
PassengerNodejs /home/user/wrappers/node
# Nginx
passenger_nodejs /home/user/wrappers/node;