I was going to get into the wording but it's taken care of so I'll just echo: your attack isn't over until the secret triggers, because "when" means the damage dealt must be traded before the attack is technically over, so it's working correctly.
It's a tough card to beat sometimes. I've lost to it more than I care to count, but that's just Hearthstone sometimes.
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Rage quitting: the best way to ensure your opponent knows they beat a giant baby.
But yes, I wish they change it so that Flare wouldnt get Counterspelled...
Slightly off-topic, but I agree with this so much. I love mage, but this interaction is so silly.
It would be weird for them to fix this, though, since the cards are behaving properly, unless they printed an extra line on Flare that said "cannot be countered".
A tad specific though.
They could change it to a 0/0 weapon (Called Flare Gun) with a battlecry that destroys all enemy secrets and draws a card. Counterspell problem solved! (but it would create some odd weapon interactions)