Clarification ...

Matt, I'm not sure what dictionary you are using, but the word church is most definitely derived from the Greek word ekklesia. That is not to say that there are no other words that get translated into the English as "church," but ekklesia is one of the roots coming out of the koine Greek. One possible reason that your dictionary may not reference it is because koine was essentially the "street Greek" of the day. It lacks the sophistication and nuance of more formalized Greek which is generally referenced in dictionaries. In fact, if I am not mistaken, the Bible is the only significant text we have the records the "language of the day" as it were. Anyway, if you are looking for an easily accesible dictionary addressing this issue, I would suggest either Mounce's Basics of Biblical Greek or Interlinear for the Rest of Us: The Reverse Interlinear for New Testament Word Studies.

As to whether Christ would have preferred someone other than Ceasar to be running things, I don't know what to say to that. On one level, you have to go with a resounding "yes," because God generally opposed people masquerading as gods and saviors. On the other hand, what men intend for evil, God purposes for His good. So yes, Christ would prefer people don't go claiming salvation through politics, but at the same time used someone who was doing this to accomplish the purpose of His own death.

Either way, the point stands that our identity is directly wrapped up in the political world. We were told to gather in places (ekklesias) that stood in defiance of an evil political system that was built upon communities (ekklesias) that recognized the authority of that evil system. As such, we are called to stand against evil acts committed by this world.