Does the Degreaser affect the afterburn damage of the Flare Gun?
No.
Each individual weapon's special effect only corresponds to only that weapon, not the entire player loadout. It's just like although the Rocket Jumper has -100% damage penalty, you can still kill other players using Melee or Secondary Weapons (it's one of my favourite loadout - Rocket Jumper, BASE Jumper and Market Gardener).
So yeah, your Flare Gun will still have the same damage and afterburn damage as before.