Right now they alternate back and forth between caring and not caring about PC games, and the mixed messages have just further confused things. But don't worry, by all accounts they've screwed up nicely with Kinect too (hence the $300 million marketing campaign).
Interesting, I've now heard three different numbers for how much they're spending on marketing Kinect; $300, $400, and $500 million. I don't see why spending that amount of money indicates Kinect will fail. Given their past with phones, as you mentioned, I would think that if they see Kinect as a failure they would quickly drop it and try to sweep it under the rug. They could be trying to hype it up to the point that everyone has to have one, but I don't get that sense.
Mind you, I still think Kinect will fail, but because it is overpriced. It's a pretty cool piece of technology, and it wins points over Move for not being a shameless copy of the Wii, but $150 is just too much. If Microsoft agreed with me on this, though, I don't think they would be planning to spend so much marketing it.
Anyway, to get to the point of the OP, I don't think Microsoft (willfully) tried to harm PC gaming. Consoles in general just have more advantages that make them more attractive (not to say PCs don't have advantages, they just aren't as big in comparision).
Xia already mentioned uniformity, and this is huge. On consoles, developers don't have to spend a lot of time and money making sure their games work on a wide range of configurations, and players don't have to worry about meeting any sort of minimum requirements. Some will argue that is just console gamers being lazy and stupid *coughMylescough* but when most people just want to blow something up/kill something/raise an empire/etc they don't want to bother making sure their graphics card is compatible, or that their drivers are updated to the right version, or that their brand of mouse is compatible with the game (I've had a problem with a game where it didn't recognize the scroll wheel on my mouse, so I couldn't zoom). Consoles make everything easier; PC gamers are just used to it being hard
The next big advantage in favor of consoles is price. Yes, PCs can be used for more than just gaming, but that doesn't change the fact that they are more expensive. Look at it from the prospective of a parent (ie, the people buying games without doing significant research) buying for a kid's birthday/Christmas/whatever; you can buy them a $700 PC or a $200 Wii. Which would you choose to buy for your kid? It doesn't help that consoles are slowly adding capabilities that were previously exclusive to PCs, like streaming video from Netflix or other places and surfing the web. Throw on a printer, word processor, and a keyboard and you could do pretty much everything with an Xbox 360 that most people use their PC for.
Again, all of that is not to say that PC gaming is inheritly inferior to console gaming or that PCs do not have their advantages. It's just that from a developer and publisher standpoint, the advantages of consoles (low price, uniformity, stability) outweigh the PC advantages (modding, openness). Modding is great, but except in very rare cases it's not going to move units of a game very significantly.
None of this would change if the Xbox had never been released. Microsoft is not (and was not) trying to kill PC gaming, but it hasn't done much to help it either.