The problem I have is that you keep saying "linking" is prohibited. The regulation only says "connecting to a network other than for control purposes" is prohibited. Although a network is the most likely (and easiest) way people would link repeater, it's not the only way. Two repeaters could be directly connected (linked) which would not involve a network.
Also, the fact that probably hundreds of GMRS repeaters are linked, using the internet, and FCC has done nothing about it, including no "do-better" letters, makes me think it's a tempest in a teapot.