WHOA, guys - it's possible that the dealer heard you say "ECU reflash" or reprogramming and didn't know that the ECU reflash you were talking about was from Mazda.
If you flash the computer with NON-Mazda code (or run an aftermarket engine management system), the dealer is right, it'll void the engine warranty in a heartbeat IF Mazda an prove that the reflash caused the damage (and, chances are, if you're running non-Mazda code you're pushing the engine pretty hard and it certainly WILL void the warranty.). Can't blame Mazda or the dealer for that.
If, however, the dealer had known that the reflash was a Mazda-recommended fix, they probably wouldn't have reacted this way.
It's only if they
(a) know the fix was from Mazda and
(b) still reacted this way
that they're morons and, given what I've seen from some dealers, this is certainly quite possible. Call them again now that the "fix" is better known.
Remember - dealers (and the humans therein) are very accustomed to dealing with angry customers. Most are taken off-guard and can be easily won over (rightfully so) with a calm, reasoned, professional, factual approach.
Oh - and a phone call or letter to MNAO helps sometimes.