it's been debated (in my original intention Prone targets could not Parry at all) and in the end we decided that yes, prone targets should have a modifier. I altered the text:
Parry does not protect from Flails, missile weapons or spells (including spells with the Melee tag), or the Headbutt and Shield Rush Traits. A Prone model has -1 on his Parry rolls, and may turn a Recoil or Knockdown to a No Effect, but a Kill or Gruesome Kill may not be reduced.
This will still let models with Expert Parry, or high Q, to deflect a minor blow while Prone, but a serious blow will still kill the character.