How to safely change MySQL innodb variable 'innodb_log_file_size'?
Yes it is safe to delete the log file once mysqld has been shutdown

In light of this, just perform the following steps:

mysql -uroot -p... -e"SET GLOBAL innodb_fast_shutdown = 0"
service mysql stop
mv /var/lib/mysql/ib_logfile[01] /tmp
service mysql start


Starting up mysqld will recreate ib_logfile0 and ib_logfile1

Give it a Try !!!

UPDATE 2011-10-20 16:40 EDT

It cleanly page out all data in the InnoDB Buffer Pool prior to redoing the Log Files, you should set this option about 1 hour before shutdown:

SET GLOBAL innodb_max_dirty_pages_pct = 0;


By default, innodb_max_dirty_pages_pct is 75 (MySQL 5.5+) or 90 (prior to MySQL 5.5). Setting this to zero keeps the number of dirty pages under 1% of the InnoDB Buffer Pool. Performing service mysql stop does this anyway. In addition, a shutdown will finish up any remaining items in the redo log. To keep to this option just add it to /etc/my.cnf:

[mysqld]
innodb_max_dirty_pages_pct = 0


UPDATE 2013-04-19 16:16 EDT

I updated my answer a little more with innodb_fast_shutdown because I used to restart mysql and stop mysql to do this. Now, this one-step is vital because every transaction uncommitted may have other moving parts within and outside of the InnoDB Transaction Logs (See InnoDB Infrastructure).

Please note that setting innodb_fast_shutdown to 2 would clean the logs out as well but more moving parts still exist and gets picked on Crash Recovery during mysqld's startup. Setting of 0 is best.