The Humble Store still has Steam keys for D:OS, and any retail releases of the game are Steam. D:OS keys created before the EE was released should also give the EE when redeemed.
https://www.humblebundle.com/store/p/divinity_originalsin_storefrontI think the original intention was to delist D:OS so it wouldn't come up in a search, but not to remove the game entirely. Someone looked into that, and the Steam store page for D:OS was restored, but not the buy option, so I'm guessing it wasn't possible / feasible to re-list the original version.