The movies attempt to portray realistic warfare scenarios that, up until TF: Prime, had never really been reflected in most of the TF cartoons. There had been shades of it here and there in some of the cartoons, but the movies were really the first motion pictures of the brand to really hit home with the concept. While the cartoons did speak of the conflict being a war, it was mostly depicted in the style of what superhero genre stories had come to be like, rather than really taking the concepts of war and warfare to heart, for the sake of appealing to young children without bringing down the wrath of unhappy parents and/or other authorities.
Since the movies were really the first really big and really mainstream TF thing to strive for actual war genre levels of violence and situations, they also went with a portrayal of Optimus that's more evocative of a real life soldier leader over the more child-friendly superhero commander that he had come to be known to be like in all the years before. In real life, the "good guys" don't just let the enemy get away to keep fighting another day after some harebrained scheme of there's was foiled; they fight to the bitter end. Thus, Optimus takes far less prisoners in the movies and has a much smaller conscience about killing his enemies in general (not just about killing them when they're defenseless, but even about killing them in battle as well, which itself rarely happened at all in many of the pre-movie cartoons).
Lots of people point to the season finale of Animated as an example of how Optimus should act in the movies, in which he chose to take a defenseless Megatron prisoner rather than killing him since "That would be the easy way out." In a perfect world, yes, this would be a more ideal way to depict Optimus in the films. But since the threats portrayed by the movies have come to be on the levels of Kryptonian invasion in
Man of Steel, it is relatively impossible for Movie Optimus to simply disable and capture every onscreen Decepticon without killing them since the movies made the Cons so inhuman and monstrous that they're all too dangerous to be kept alive, and the Movie Autobots likewise lack the means to properly incarcerate all of them. So the movies have purposely written themselves into a corner that prevents Optimus and the Autobots from going with any less violent methods short of killing all their foes. And since many viewers were evidently turned off by seeing their childhood icons be portrayed like violent soldiers involved in these scenarios that more resemble real life combat rather than classic superhero combat, Movie Optimus is thus looked down upon as "less noble" and "less heroic" than several of his more superhero-esque pre-2007 fiction counterparts.
Whether this is actually true or not is and has been a subject of debate since the 2007 movie, and will likely continue to be for debates yet to come, as there is simply no right or wrong answer here since everybody views heroism, nobility, and ethical nature of each in different lights and often tend to find very few common grounds of agreement, as there are those who prefer the more realistic take that the movies went with while others prefer the more child friendly classic superhero take that had been in effect since 1984.
And after having said all that, there's now the elephant in the room that is the "realistic superhero stories" like the Nolan
Batman trilogy, the aforementioned
Man of Steel film, and other examples that the TF movies
do resemble, which helps to make the whole above explanation bare less weight. But if one considers my occasional use of the phrase "
classic superhero" to refer specifically to the more child friendly iterations over the more realistic ones, then that might let this argument prove more fruitful.
