I don't really think this damaged their reputation, even in the slightest way. I had never heard of the problem, and it seems that even the people that suffered it went ahead and bought another mac: https://news.ycombinator.com/item?id=9079010
Because Apple bundles everything (and refuses to unbundle the OS from the hardware in any way), you are likely right that the effect will be minimal because the benefits of all the goods (bundled together) outweighs the costs (and consumers have no choice -- if they want any part of the bundle, they must buy all of it).