How do I enable InnoDB on a MySQL-EBS server?

Answer

You need to delete or move the stale logfiles to allow InnoDB to regenerate them and restart mysql: 

~# service mysqld stop
~# mv /var/lib/mysql/ib_logfile0 /var/lib/mysql/ib_logfile0.bak
~# mv /var/lib/mysql/ib_logfile1 /var/lib/mysql/ib_logfile1.bak
~# service mysqld start
~# echo 'show engines;' | mysql

The last step will display that InnoDB is enabled.