Well Mat does die during the attack on Caemlyn when Rahvin used a lightning attack. But on the flip side Alivia was unharmed by a fireball hurled by Cyndane ... Perhaps the weaves that make lightning simply stimulate a natural bolt of lightning while the fireball is truly a weave. Which would indicate that Balefire would not effect Mat unless the weave somehow creates a natural reaction that triggers Balefire... Which would mean Balefire is in some way a naturally occurring construct rather than simply a weave.

So many little contradictions in the books that it makes it impossible to say for certain ... Essentially it was left to RJ discretion in a given situation.