This is often criticised, the thing is, in the name of progress it happened all the time. The Sopwith Tripe didn't just get copied by Fokker, almost every company began triplane designs and Fokker's was certainly not the first or only triplane to emerge subsequently.
Fokker's decision to go with a wooden box spar design of cantilever wing as opposed to going the metal route, which he could have under the terms of the contract, was not only sensible, it was timely. It could be produced on existing lines by existing staff without retraining in metalwork techniques and therefore it could be applied quickly and effectively. Junkers, while novel was hampered by practically inventing an industry. He pioneered metalwork on aircraft construction, the use of compressed air riveting tools, swaging metal fittings etc. His firm first put that stuff into use. Germany didn't have time or the resources to put that into action across the entire industry. Quality aluminium was not freely available and the workforce on the whole had never built metal aircraft.
It wasn't until after the end of the war that, concentrating on civil aircraft, did things change for Junkers. The production of the J4 couldn't been done without the Fokker company's industrial knowhow or support, and it put Junkers into a position post-war to become a major supplier of transport aircraft around the world.
The government was right to force Junkers to work with Fokker; it was prescient as it did see the potential of what was on offer but it couldn't be taken advantage of without input from an industry giant.