Bill Gates didn't do that as some sort of goodwill gesture, he did it because he felt it was right for MS.
Wasn't the money put into Apple part of a deal after Microsoft was found with source code for Quicktime getting into their own video software?
The "Microsoft believes in Apple" from that might be more Job's reality distortion field. :-)
But going back to the original point, if that's true you could say that Apple was in a slightly better state than it might have appeared (in that it had leverage over MS that it could use that might not have been obvious at the time) but I don't think it significantly undermines the idea that Jobs did a fairly remarkable job in turning Apple around.
After all, MS and many other companies had far more resources than Apple even with the settlement and none of them had the same level of success Apple enjoyed during that period (or since).
To me at least, what makes Jobs most interesting is what he achieved despite being an asshole and how that played out. He undoubtedly was a thoroughly unpleasant individual and people who worked with him will queue around the block to tell you that, but he also, coming from a pretty low baseline, turned Apple into the largest company in the world by getting many of those same people who will tell you he's an asshole to build genuinely great products.
The most interesting people are rarely one thing or the other - that's what makes them interesting.