Yes, Microsoft has an enormous amount of money, but not because they spend it stupidly, and the people at Microsoft responsible for overseeing Remedy do not have access to all that money.
Ahem. MS has a track record of throwing away money in an attempt to hurt the competition. That's why they pay top dollar for timed (usually for a month) exclusivity. Remember the GTA4 DLC? $50 million for timed exclusivity. I imagine they're paying something similar for CoD DLC timed exclusivity. Probably a little less for Skyrim DLC timed exclusivity. And you know all those ads for multiplatform games that show the Xbox logo at the end and make no mention of PS3 or PC? That costs MS money as well.
The money dried up and Remedy cut the PC version because they did not have enough cash to complete both.
That's not how it works. Developers don't get to decide which SKUs to cut. That's a publisher decision. They fund the game and they decide which platforms it gets released on. MS cut the PC SKU because they wanted the game to be an Xbox exclusive. It's as simple as that. Hell, the only reason it was ever even announced for PC in the first-place was because development started before the X360 was released. If it had started later, it would have been an X360 exclusive to begin with.