Option B: Change your Windows architecture. You can run Windows applications from a terminal server like Citrix. Or virtualize them with Softricity. Or move everything to blades. Yeah, it's a pricey transition, and it'll shake up users. You'll also probably need a lot more network bandwidth. But rebuilding all those PCs will be easier if it's ever necessary.
Option C: Abandon Windows. Whether that means Web-based apps or Linux or Macs or terminals, it's likely to be the most disruptive and costly option in the short term for both users and IT, and it will radically change what your IT shop does.
None of those options is a true trade-off. The cost and effort is all ours. We're facing complex and expensive choices, with no certainty that we'll ever see the underlying flaws fixed. Right now, it's all Microsoft can do to fix surface-level problems like buffer overflows.
It's going to require a completely new Windows core to finally purge the rootkit cancer for good. And that's going to take a very hard, very expensive decision by Microsoft.
Not just the worst of work-arounds for us.