I would use them, personally. nVidia cards do better for linux gaming than AMD, so your plan for passthrough (at least for the games that the 680 can't effectively play native in linux) is a good one imo. Giving the spare to your brother (or lending it to him until you need it later on) is a good idea too. As long as the hardware is getting used, then good.
If keeping both is an option, and you are willing to fiddle with drivers, thats really a lot of gpu power. You don't get perfect scaling in sli and cfx, but if you want to compare the amount of compute you'd be getting 13000-14000 in firestrike points with the 680's and 8500 with the R9 380. There is a lot of power there, so I would say try the the 680's in your system and see how your suite of games plays with sli. If you have them, try them out and see how those cards behave with the games you like to play. If it doesn't go well, sell one and use the 380.
Just discovered that my Asus P9DWS motherboard doesn't support Nvidia SLI. Only 4 way CFx. So I'm testing the Gpu pass through thing with KVM. It's hard, but I'll make it work. Thanks for the suggestions!