I believe that we have here two different subjects. The first would seem to be validated by the words of Jesus regarding his Kingdom of God program. These writings seem to emphasize personal interactions on an immediate level, as does Mosiac law. What can you do here and now to help the poor and suffering and prevent discord in your community. External "enemies" or oppression is to be either ignored or complied with to the extent practical for peaceful living. But it asks for something beyond mere tolerance; it requires that a person's position relative to you be carefully considered. Love my enemy? Why? How does that help me? Like many of the sayings of Jesus it is (at first) counter-intuitive.
The second subject regarding the actions of the church seeks to apply legalistic self justification to the actions of this corporate entity. To the extent that humans have a history of twisting the meaning of philosophies to the ends of greed and fear the church (which is not part of the Kingdom of God movement) can certainly cite this saying as it chooses. Christendom or the church at this time is the most powerful entity in the western world. It's actions and interests are political and economic on a sweeping geographical scale. What the church does and says is really not concerned with what Jesus actually meant but how it can help them achieve control and protect their investments. At this stage in history (the crusades) the church is no more about the teachings of Jesus than a giant waterfall is about the bubbling spring at it's source.
So it seems both interpretations can be "true"...however actually unrelated.
Patriotism is the last refuge to which a scoundrel clings...Steal a little and they throw you in jail, steal a lot and they make you a king
The political theorist Carl Schmitt argued that if one consults the Greek of the Gospels, one finds that Christ's command to love ones enemies reads "diligite inimicos vestros and not "diligite hostes vestros".
In Greek inimicos signifies a private enemy, wheras hostes means a public enemy. So when Christ tells us to love our enemies, he's telling us to love our personal enemies.
This is why, as Schmitt argues, there was no contradiction in Christians waging war against the Muslims with the Gospels because the Muslims represented a public enemy to Christendom.
As Schmitt noted: "The enemy in the political sense need not be hated personally, and in the private sphere only does it make sense to love one's enemy, i.e., one's adversary."
It's dangerous to draw conclusions from what is NOT said, and especially in a document as old as the gospels (there are historical and cultural factors that can further cloud the meaning). This just sounds like an extension of attempts to reconcile the God of the old testament vs Jesus (where Yah_eh destroys Israel's enemies, and Jesus is all about the love... roughly). It does not make sense to only love your private enemies... it doesn't fit with anything I've read of Jesus.
EDIT: I'm intentionally overlooking what Jesus meant by "love"... that's a whole other discussion.
"OMG I FEEEEEEEEEL SO INTENSELY ABOUT EVERYTHING OMG OMG OMG GET ME A XANAX" -Priam (ENFP impersonation)