The risk here is very different with Microsoft Windows and MAC OS X than with GNU/Linux.
1) In the case of Microsoft Windows what the OP describes is very easy to implement, since the operating system is propriety software. It is easy to keep this quite until the date and time of the attack. The patch is included in a software update from the "trusted" vendor Microsoft and delayed in effect in order to maximize installation. With over 90% market share in the desktop the impact on Bitcoin would be huge (knocking out the vast majority of nodes for example) but not fatal (see (3) below). We must also keep in mind that since the advent of the DRM in Windows Vista
https://en.wikipedia.org/wiki/Criticism_of_Windows_Vista Windows Administrators do not really have the equivalent to full root access since certain processes are "protected" in order to enforce the DRM as per the MPAA's etc requirements. The paper by Peter Gutmann is very relevant here.
http://www.cs.auckland.ac.nz/~pgut001/pubs/vista_cost.html. The situation is getting way worse with Windows 8. It is fair to say that Microsoft Windows is the single biggest vulnerability for a centralized attack that Bitcoin has, and it is not just governments we have to be concerned about here. An attack by a criminal / terrorist organization that finds a vulnerability in Microsoft Windows is far more likely and could be equally harmful.
2) As for Mac OS X the attack under (1) is possible since again the operating system is for the most part propriety. The one difference from Microsoft Windows and also from its mobile cousin IOS is that it is not as infected with DRM at the OS Level as Microsoft Windows or IOS. Maybe an Mac Expert can clarify this but I do believe that root in Mac OS X is for real. So the attack is possible but harder and easer to defend against. Because of this and the low relative to Microsoft Windows market share of Mac OS X, I would consider the impact of Mac OS X here to be neutral.
3) GNU/Linux. The attack here is very unlikely because of a) The software is Free Software / Open Source so if a binary does not match the source code alarms will sound all over the place. There are literally hundreds of GNU / Linux distributions all over the world. c) Each component of the Operating System is maintained by thousands of different individuals, projects, corporations, and organizations all over the world, many of which have very radical and opposing views. Good luck keeping a secret to coordinate this among the likes of
both Richard Stallman and Linus Torvalds for starters. The secret would be out long before any implementation so an attacker would find it in their best interest to limit themselves to Microsoft and its
proprietary Windows operating system.
The real question becomes will Bitcoin survive if most of the Windows users and nodes are knocked out? The answer is yes there are enough GNU/Linux users around to ensure Bitcoin's survival so the attack will fail. One possible consequence however is that some of the GNU/Linux users may become very wealthy at the expense of some Microsoft Windows users in the resulting panic.
The best defence here is simply to stay away from proprietary software and operating systems when using Bitcoin. Here is a list of effective antidotes:
http://prism-break.org/