We just have to be careful the tourneys wouldn't be abused
Another thing gems do is prevent clans from somehow abusing the system to exchange resources. Now I know we wouldn't be in control of who we are matched up against but we do have to consider this possibility. We can't have any system that can be used to exchange resources. If enough safe guards are in place then I guess gems could be avoided for the entry. As an alternative, the entry in gems could also be much lower than I first outlined.
As for letting the leaders decide match-ups i hear your concern. But I would want a system where the leaders actually lead. I think this would make clan roles more significant - another feature people desperately crave.