I used a wget script for a while to patch, but for the reasons mentioned above it's not very effective. (As I DC now 95% of the time, I don't play in Linux anymore anyway, though...).
As for a more open patch method.... Isn't the whole 'patching' side of things the only illegitimate side of SoD?
I guess what I'm saying is that some way of patching effectivly minus the windows .net method would indeed be great.
(ps. I think there are various links on the forum to 'fresh' up to date patchfiles, how often these are actually up to date idk...)