I highly doubt any tune will cause permanent hardware damage. I've seen too many times shops don't know what the cause is so they blame the "software". Exactly what is wrong with your car? What year? There have been a few DME failures lately, it is starting to look like the new HPFP for those build dates.
99 Eclipse GSX dyno numbers soon
12 Maxima Slow
03 EVO 8 600HP Sold
09 e92 335i 440hp Sold