nybbel41's arguments may be of use to a defense lawyer (so long as the lawyer is also aware of likely counter-arguments, possibly including some of the below); whereas for anyone concerned about infringement, the important thing to consider is that the advice in the Debian patent policy FAQ was prepared by lawyers, whereas nybble41 hasn't claimed any legal credentials or cited any cases or other legal opinions.
Re source vs. object code: the FAQ itself gives reasons for the (tentative) conclusion, which nybble41 doesn't address. It's also a bit harder to argue that x86 object code is provided for explaining the invention rather than execution (practice of the claims).
If the "general-purpose computer" argument is valid, then there's still the problem that Free Software is increasingly being used on non-general purpose machines. One should also consider some of the patents that US courts have upheld, which might make one doubt the safety of even the "general-purpose computer" argument.
Re "isn't implemented until someone actually runs the software", there's in any case still the concern of inducing infringement or contributory infringement.
Again, IANAL; sorry for commenting on things I know little about.