And now I'm personally offended.
I'm not going to even argue about how you're depicting "Country A"'s military strategies, ability to deal with civilians and unknowns, and general sanity, since it would only result in me getting madder and pretty much ruining everybody's day, so I'm just going to talk about the obvious plot holes. You say that Gensokyo can only be accessed through the Hakurei Shrine: so how the hell did all of those soldiers get there? Rumia was encountered before Reimu and Suika, so obviously that one soldier got in somewhere else. Also, again, there's the issue of communication apparantly working through the barrier. For that matter, how the hell did the helicopters and the planes delivering payloads of napalm (and the mere issue of using napalm on Japanese soil is a whole 'nother can of worms) get there?
So, my advice: save face, and don't bother trying to pass this off as being a serious story. It works as an absurd humor story, but once you try to apply it to reality (with some willing suspension of disbelief, considering the whole nature of Touhou), it breaks down, hard.
Wow, you're right, and I'm really sorry. I messed up big time. I could (and perhaps should) add some chapters to the beginning, and change when Rumia appears. Truthfully, I don't know anything about military strategies, but I knew that I had to include them since the real world would obviously take an interest in this incident. Heck, some of the strategies are (lovingly) ripped right from Call of Duty.
Now, the entrance to Gensokyo is the area around the Hakurei shrine. Enter any other way, and you won't get in, in fact there wouldn't be anything there. After a while, the military figured that out, and have been using that hole in the barrier to do just about everything, from sending helicopters and troops to communicating. They aren't actually communicating through the barrier, but are communicating through the hole in the barrier around the Hakurei shrine.
I have communicated the strategy rather poorly, and it might be a rather bad strategy, since I knew I needed the army, but didn't know much about it. Initially, they were gathering intelligence, the goal was to stay relatively undetected while finding what could have caused the incident. The soldiers didn't want to be detected by Reimu, and didn't know she was special at the time, which is why they found Rumia first (Once again, it's very open to revision). Once they realized the nature of the hostiles, they started with the Hakurei shrine, and decided to surround the major population center to cut off the terrorist escape routes before invading. It didn't work. They also wanted to capture as many enemy combatants as possible for research, rather than kill them. But I agree, the strategy is questionable at best.
I guess I should continue writing it as an absurd humor story though.