I'd have to experiment with it again, things might have changed in a patch since then but I do recall Grenades, Flame Pillar, and potentially fair just clanging the move. Grenades might no longer do this, but I semi doubt it if Flare Blitz has remained the same more or less throughout the patches.
~I did it~
Projectiles that will stop / clang Flare Blitz:
Charged Shot (Medium Charge and Above)
Flame Pillar (At all times)
Stealth Shot (if timed correctly)
Bomb Drop (Still hits Gunner if used on ground)
Grenade Launch (If not yet exploded, will still end move during start-up though)
Flare Blitz goes through the remain moves at all times.
Fair
Charged Shot (Below Medium Charge)
Laser Blaze
Grenade Launch (During explosion)
Gunner Missile (Both Variations)
Lunar Launch
Considering that pretty much any Mii Gunner trying to play their character decently is going to avoid Laser Blaze like the plauge, Charged Shot and Grenade Launch are more than likely always going to be an answer to Flare Blitz. So there's that I guess.