Charlie Morton is a 3rd year salary arbitration eligible player. Lets take a look at what similar pitchers earned. I looked for pitchers who were coming off injury shortened seasons or had a similar 2nd year arbitration salary as Morton. Of course keep in mind that Morton's second year salary was low based on his coming off Tommy John surgery in 2012.
Morton's 2013 salary 2M
2013 116INN 7WINS 3.26ERA 1.28WHIP 6.6K/9 0.5WAR
Career 589INN 30WINS 4.70ERA 1.50WHIP 5.9K/9 -0.7WAR
2012
J. Sanchez 2011 Salary 4.8M 2012 Salary 5.6M
2011 101INN 4WINS 4.26ERA 1.44WHIP 9.1K/9 0.0WAR
Career 708INN 38WINS 4.26ERA 1.39WHIP 9.4K/9 6.0WAR
Brandon McCarthy 2011 Salary 1M 2012 Salary 4.275M
2011 170INN 9WINS 3.32ERA 1.13WHIP 6.5K/9 3.2WAR
Career 543INN 29WINS 4.17ERA 1.29WHIP 6.2K/9 7.1WAR
Jeff Karstens 2011 Salary 1.1M 2012 Salary 3.1M
2011 163INN 9WINS 3.38ERA 1.21WHIP 5.3K/9 2.7WAR
Career 501INN 21WINS 4.52ERA 1.37WHIP 4.7K/9 2.9WAR
2013
Edison Volquez 2012 Salary 2.23M 2013 Salary 5.725M
2012 182INN 11WINS 4.14ERA 1.45WHIP 8.6K/9 1.0WAR
Career 679INN 44WINS 4.52ERA 1.48WHIP 8.6K/9 4.2WAR
Jason Hammel 2012 Salary as 3rd year super 2 4.75M 2013 Salary 6.75M
2012 118INN 8WINS 3.43ERA 1.23WHIP 8.6K/9 3.0WAR
Career 850INN 42WINS 4.78ERA 1.44WHIP 6.6K/9 6.9WAR
When looking at these numbers keep in mind a few things. Both Sanchez and Karstens did not finish the 2011 season due to injuries which presumably kept their 2012 salaries down. Morton on the other hand missed time early and was healthy at the end of the season.
The other thing I can't quite understand is how with very similar numbers across the board Jason Hammel gets a 3.0WAR and Morton gets a 0.5WAR. Also Karsten's career numbers are marginally better than Morton's yet he has a career WAR of 2.9 while Morton has a career WAR of -0.7. This small sample size makes we wonder if WAR for starting pitchers is a good measure of value. I would welcome any comments from those more versed in sabremetrics if and how WAR should be applied to starting pitchers.
Based on the above I would expect Morton's salary to be about 5M next year.