Obsidian sanctum would still be locked only for players who are in same matchup. How would it make better sense?
To get into Eotm gvg arena you have to go through portal, it is not connected to other parts of map, it doesn not interfere with your beloved eotm map. Some of the players didnt even know that such area existed.
Eotm was designed as a waiting room map for main WvW.