At the end of the say, you can make any argument, but to say that Joel's actions at the end were evil--that's just not a reasonable one. For example, if he were evil, he could have just let her died and walked away at the end. Whether you agree with Joel or not, it's clear, in my opinion, from the first act to the last, that he's acting as a parent. It helps to see this if you are a parent yourself.
As for her age, Ellie is 14, not matter what she's been through. The game is full of examples that show she's just a child, from giraffes and the like. Just because a child has gone through traumatic episodes does not make her all of a sudden have the mind and mental capacity of a 19 year old. In fact, just the opposite, PTSD is common in such instances and many children actually regress to a younger mindset than their actual age.