You're right, there will probably some resistance from the publishers who happen to also have a store on Windows. But it means looking at SteamOS just as another distro, competing with Windows. Or we know SteamOS is madly bipolar and when bundled with a Steambox can be considered as a console, or "a new system to play games in the living room".
Technically speaking nothing prevents EA and Ubi to port their games on Linux, They already make ports for a thousand machines, if they think the userbase is /will be important enough to recoup their cost, they will want to do it. What may prevent them doing so is your argumentation and my first paragraph. however there is a third way that could be explored.
Publish games on Steam for SteamOS only. No cross-platform. Games can be bought on Steam but can only be played on SteamOS (just like we can already buy games on Steam and only play them on Windows). If the user wants to play them on Windows they have to buy on Origin. (Possibly make a gracious SteamOS key offer on Origin and at retail?) EA and Ubi are already perfectly contempt publishing on consoles, which don't sport Origin nor Uplay stores and have them fork a bit of their money on digital.
SteamOS port would be seen as "just another console port", would not invade the Windows only Origin market, and Valve would be happy to have its userbase grow. This is pure speculation on my part obviously but such a way would bring more money for both parties while not take a cut from Origin. I'm pretty sure right now Valve only care for crossplatform to go Windows -> Linux but have no interest at all to have it the other way around. i find such a deal with EA (we'll publish on SteamOS if you leave us the Windows space) perfectly reasonable.
