Generally speaking, IC can be prone to heat damage when they find themselves at the end of a hot tip... best IMO not to risk it.
That said, if you are able to program it, seemingly without errors, then my guess would be that the chip is fine.
FWIW, I was able to program a Uno following the tutorial you refer to, using the manual method of compiling a 'blink', so it seems to work as described. I used the reset on bcm8 to be as close to your setup on the Pi side.
... I'm going to dig my AVR 'shrimp' and see if I can get it alive, though I'll have to do some mods to bypass the caps, so I can test something as similar to your barebone AVR.