The article you pointed out nowhere mentions that it was hacked via gps spoofing. Infact it is not exactly known how did the UAV crash, and there are many theories. Moreover these UAV's wont be completely dependent on GPS, more tools may be used in tandem such as VOR/DME/TACAN etc. But we wont know it for sure because that would be classified info!
You can control an rc aircraft irrespective of a gps module because that would depend on your radio range. Gps only provides you location and helps you/AP in navigation. And IMO everything is hackable, just need right kind of people to do it.
Now everything you are asking has already been done with some rc grade stuff and items are available including encrypted video tx/rx , so is long range tx/rx. Homebrew antennas with tracking can take care of extreme long range.But fact is does defense forces really want an assembled rc craft made out of off the shelf items widely available? Because anyone with intermediate rc skills,trial and error, can assemble it. Results of similar militarized version of RC grade North Korean drones
http://www.suasnews.com/2014/04/28529/n-korean-drone-crashed-in-gangwon-last-year/http://www.suasnews.com/2014/04/28519/third-drone-found-by-wild-ginseng-digger/If you are really making something for defense forces then it should be something indigenous wherein you can get a final product according to your specs which inturn decreases chances of getting hacked. Using hobby grade stuff is a very bad idea. There are many more things that would go into designing Military grade UAV but Im sure you would know about it since you are working on it!
And Im more scared now since a defense contractor(?) for forces is asking such questions on a public forum
Feel so bad for the forces and wonder where they are heading