Same result, without long backup times, Apple server bandwidth usage and your iCloud storage usage.
I don't care how Apple (or Marco) solves the problem, but I sure do not want to lose Instapaper articles at random.
I think that has to be the best solution. It's far better to just have everything sync to iCloud and let the user choose to disable it rather than having Instapaper's primary core functionality - being able to read articles offline - not work properly.
My premise, in point #2, is that this actually isn't the case with respect to Instapaper's raison d'être. In fact, that's sort of the premise behind much of Marco's post too.
That's kind-of the issue though, is it not? One of Instapaper's strength is that it provides for reading in a nicely formatted and offline way. You don't need a connection to go through your IP stack, unless iOS has decided to clean out everything.
His point is, if you back it up to iCloud, to get any use out of the backup, you need to be online. Therefore it's a waste, because in that scenario, you can just download it from Instapaper anyways.