There's no defence against Mediggo Flame. The only way to survive is to have 9999 HP. Mediggo Flame always deals 9998 damage to everyone, unless they're invulnerable (Hero, Hero+, Holy War-trial or Holy War).

My strategy is similar to yours.

My party consists of Squall, Irvine and Zell, with junctioning to take their strength up as close as possible to the maximum.
Once the fight starts, I immediately summon Cerberus, or simply cast Triple on one of my characters. I then cast Aura on everybody, then use a Holy War.
The next step is to cast Meltdown on Omega Weapon to remove its physical defence. From then on, the strategy is simply: limit breaks, and lots of them. Thanks to Aura, every character can use a Limit on every turn; even if the limit icon doesn't appear, simply push the 'change character' button till it does re-appear. Every hit from every limit break should do 9999 damage, except if you're using Irvine's Fast Ammo. With Zell, you can do up to 15 hits at 5000 damage by using the 'Armageddon Fist' technique: Simply use the two weakest moves (Punch Rush and Booya) over and over. They take only a fraction of a second, so you can do some serious drubbing.