You are putting way to much thought into it and making it convoluted when it isn't, the individual militant is a person working on their own, a small group can be self sufficient however when you start getting to larger size organizations they need differing types of support networks and when it comes to a military they need something else entirely. If you view it as business from the self employed to the international corporation you can see the differences, but they are the same thing just of a different size. The IDF was created as a defense but to defend there ideology and protect why they are there in the first place, and sadly as the Israeli leadership is starting to become more fundamental I wouldn't be surprised if they keep becoming more and more aggressive in pursuit of these, luckily Obama is currently holding them back at the moment but maybe not for much longer depending on the presidential election.
I'm going to admit that we're at an impasse and agree to disagree on your use of the word "militant".
It's difficult to judge one side or the other more wrong in the Israel Vs. The Rest of the Middle East saga. I've read Moshe Dyan's autobiography which details a lot of the history of Israel (decidedly from the Israeli PoV of course) and I've read a bit here and there beyond that. I do understand the plight of the refugees and I sympathize. They are pawns of the rest of the ME and a constant thorn in the side of Israel.
There is no easy solution. If there were it would have happened in the last 74 years.