It would obviously take some tweaks to the system to get around this, but I can think of a simple adjustment off the top of my head:
For a new alliance, or one that hasn't warred for a while, use the existing war rating system to estimate their position in the hierarchy, and start them at that glory. So a brand new alliance of all atomics is given the average glory of the 10 alliances with the closest comparable war strength. Cap it out at starting no higher than 2000 glory below the bottom of the leaderboard. If it is off by much, they will quickly rise or fall. But they won't start out with crazy mismatches.
If you don't war for a period of time, or have a huge change in war weight (a 10 man alliance of medievals adding 20 atomics), then recalibrate.
Alternatively, have leagues, where your alliance war weight determines which league you start in, and then do matches by glory inside of that. Every few weeks, the top alliances move up, the bottom ones are relegated to the next lowest league. Say, 5 leagues, and a new alliance of all atomics would start at the bottom of the 2nd highest. One with mostly medievals would start at the lowest level.
Not saying they can or should do it, but there are ways to build a reasonably fair and robust system based around glory, that allows for people trying to beat the system.