I'm going to go with option 2 -- I don't think they are clever enough to nerf linux like this. They are probably just thinking, "how do we prevent viruses?"
Although that doesn't necessarily mean they're doing this out of malice, I don't think it went entirely unconsidered. MS definitely likes to be aggressive when possible.
http://en.wikipedia.org/wiki/Siege_mentality
What the Wikipedia article leaves out is that employes that are in this state will have a sort of 'fight or flight' response and will usually work their tails off.
Microsoft is hardly the worst offender in this metropolitan area, much less the industry.
you're being kind of a jerk assuming that Microsoft engineers aren't clever enough to nerf Linux like this, given its long history of hacks to both mess with its competitors (http://en.wikipedia.org/wiki/AARD_code) and make sure its software works properly (see a lengthy paper on Windows PatchGuard here: http://uninformed.org/index.cgi?v=6&a=1&p=23 and basically every post Raymond Chen makes about application compatibility on his blog here: http://blogs.msdn.com/b/oldnewthing/)
if Microsoft wanted to kill Linux through technological means, it would be able to do it. the fact of the matter is, it doesn't, or even if it does, it would never be able to convince its hardware and software partners to go along with its scheme.
Windows's support for UEFI secure boot, and its requirement that it ship turned on by default on logo-certified PCs, is a matter of reducing the number of things average people -- people who don't even know what Linux is, much less use it -- complain about Microsoft for, nothing more.
(disclaimer: I work for Microsoft, but I'm not speaking officially on behalf of the company.)
Come on. It's Microsoft we are talking about. They regularly donate software to government agencies in order to promote their lock-in and to prevent competitors from gaining a foothold.