Another fun alternative would be the Orieni finding another religion to follow. Perhaps not all of the Ancient Ones actually left. Imagine if they became devotees of a Kirishiac Lord....
Or even worse - the Thirdspace aliens/Hand!
Although, the main schism in belief systems I'd like to see develop in the Empire post-2261 is the distinctoin between those who cling to the Blessed's pro-VOrlon dogma (and subsequently are tied in to the deep related sense of loss and abandonment) and those who recognise the advent of a new era, and wish to steer the Orieni and their allies towards it.
It's good to see the Orieni get a lot of attention ,and I wish I had more time to answer some of the points raised about both the Empire and the ISA-era Minbari (look at the Minbari Federation RPG book for data on their fleet assets - they aren't as large as you might think...)
Although I did state that I would tone the Crusade down a little on both ends (they don't get as far past the Protectorate, but the ISA find it tough getting to Orien) and would make the post-coup Empire more open to interacton with the Alliance... and more active in Drakh-hunting!
One other thing - the map that the guys writing TGC were likely using is that in Rich Bax's Wars of the Centauri Republic, which includes more systems in both the Federation and Protectorate which lie 'east' of the Mongoose map, as well as jump routes we don't see in the latter. The use of these routes, as well as the Orieni seeding of new beacons, allow the Empire to reach systems like Trigati without following the longer routes seen in the Mongoose map.
And no-one got the o-r-i reference...