You're probably right, and can't have an Epic Hero join a formation without a command company, and I would agree that yes it would make siege a very deadly addition.
There are a couple of things I would like to point out though. I see where it says under Epic Heros that they should join the command company, however it does not say must. It also says in the same section that the hero can join another company close to the front as well if the command company is full. If it's ok to join a company in the back because the front is full why wouldn't he be able to join the front company in a formation without a command?
Another thing that wouldn't make sense is why have the We Stand Alone rule if you already have a formation that can't take a command company? Good example might be Castellans of Dol Guldur or Vault Wardens. They don't have a command, but then it also says We Stand Alone. If a hero can't join them because they have no command then isn't it kind of redundant to include the We Stand Alone rule? Why have the rule at all if all you have to do is not include a command in the profile?
Last is if you're right then that means the evil factions kind of get the shaft. As far as I know the evil side is the only one that has formations that can't take commands, but also don't have the We Stand Alone rule. So things like Morgul Stalkers, Feral Uruks, and Watchers are just SoL. Seems kind of suckish if like me you play Isengard 5 out of 9 Rares (not including single models like trolls and the battering ram) can't have any sort of hero with them, but don't have We Stand Alone.