Possibly. The character certainly seems to fit the archetype of the previously mentioned INFJ villains.
He exhibited a strong Fe. He knew exactly how things should be and was willing to do anything to make them so. His Fe was far stronger than his Fi. His own feelings were meaningless in the face of how he felt about the outside world, or in his case universe. "He's a believer" can be a terrifying thing to someone without beliefs.
He also exhibited a strong Ni. He knew what was going on, and never jumped to a host of possibilities or conclusions, showing an example of Ni strongly over an Ne. He seemed to be quite introspective, leaning toward Ni dominance, but how he felt about the universe around him motivated the character more than his insights. This could imply a more thinking ENFJ.
However, he seemed to have shown more Se and Ti than either of these functions. All of his actions were well thought out and enacted with precision, though motivated by a core of well developed Fe and enhanced by a solid Ni. If he wasn't a representation of an INFJ or even ENFJ with strong Se and Ti functions, he was an ISTP or ESTP with strong Ni and Fe functions. Due to the solidity of his belief system, I am inclined to type the character as one of these. INFJ and ENFJ types know what they believe, but have a lot of trouble putting it into words. We are generally only able to harm others in moments of extreme emotion. We also have a lot of trouble with guilt when we hurt others, and seldom include the right to harm others in our seemingly amorphous moral codes. This character did not exhibit those traits, leaning toward Se and Ti when they conflicted with Ni or Fe.
In any case, he did seem to be a good example of Ni, Fe, Se, and Ti, in whatever order you would care to assign them. The deciding factor is the order in which he used them. If he used Fe first, he was an ENFJ (not all ENFJs are chatterboxes). If he used Ni first, he was an INFJ (not all INFJs are inactive). If it was Se first, he was an ESTP. And lastly, the character may have used Ti first, Se and Ni next, followed by an unshakable core of Fe implying that he is best represented by an ISTP type.
However, I have to admit... this is one of the few cinematic villains I found myself identifying with on fundamental levels. If I was to go bad... it may well look a lot like that. It's likely that Joss Wheadon is an INFJ... or is frightened of us. *booga booga*
*Nods.* I think the Operative had a stronger Ni, and maybe he did show a small amount of guilt when he killed...he didn't always want to do it, and I think he dispatched his teams to do the majority of the dirty work. He only went one-on-one when it was necessary to "explain why."
And I think Joss fearz uz! I do love me some good Whedon, tho'...