Man, now i feel real unsafe, mircs good and all that,

But would you really want a program that can be taken over by a users simple ignorance of what something does, IE: they type some command, becuase the other end told them too.

Would users be that stupid? from the article "The user only needs basic computer skills to install the system" so YES users would be that stupid.
And would they trust the other end? I again say yes, it only takes one breach, and someone got control of a "trusted" nick and thus anything "trusted" nick tells you must be ok to do.
The initial hack would be the hardest thing, but once there someone could run riot.

Finally I wonder about the accuarcy of the article, "establish a mIRC server at AFCA to host the chat session", they mean a IRC server im assuming, maybe just a understanding error by the article writer, or is it more?

I would think the Military would already have there own multiuser chat system, or at least there own clients, which dont have the ability to be taken over.
Amagine a sleeper script, just quitely sitting in the room socketing out all the chat to Al and Kada at the local Kabarb shop.