Patents were a brutal business weapon seven years ago. Indeed they have been for more than a century. [
http://en.wikipedia.org/wiki/Elisha_Gray_and_Alexander_Bell_...]
However, the claim that they have recently become an existential threat is dubious, in my opinion.
Yes, there are lots of stories in the techpress about industry titans battering each with patents and partisan ranting which often accompanies it. What there aren't is stories on HN about startups forced to shutter because of patent claims.
But more importantly, funding for startups is accelerating not slowing as would be expected if software patents were a serious threat on the scale your post implies.
The problem with software patents for an investor such as YC is that they are hard to quantify as a risk and thus create uncertainty. What I see is that YC's initial approach to software patents was naive from an investment standpoint, i.e. that the risks of uncertainty turned out to be significantly greater than the potential gains from patent licensing.
I don't think YC's change was do to wholesale adoption of a FOSS ideology or conversion to Stallmanism. The day patents become a true existential threat, YC will not be funding software startups.