We cant say that he died in Ep. 1 or 2. it will be unknown till Ep.3.
EDIT: He is last seen alive in Ep. 1 departing in a train with other refugees i'd guess he is alive
EDIT: He left before Gordon and Alyx so he and the others may not have been hit by the Portal Storm.
Barney was always helping Gordon in Half-Life 2, I played it and he was a really cool guy. I don't know if you refer to HL-2 when you say "episode two" but I know he was there definitely.
He wouldnt die without getting Gordon that beer he owes him.