Thank you so much, Bob K, for slicing the Gordian knot of prepositional subtlety.
ian2, you're there, but putting "which is a sign of the times" right after "messaging" (even though they are divided by a comma) makes it sound like the messaging itself is a sign of the times, while it is their effectiveness that is the point of the sentence.
"The fact that their most effective tool was cell phone short messaging is a sign of the times."
You are right---"which" can introduce clauses that modify the entire sentence, or only part of it.
"He visited New Orleans last year, which was his first trip away from home."
"Last year he visited New Orleans, which he had always thought of as a sinful and Godforsaken city."
How can "effectiveness" be a sign of the times? If they'd tried using short messaging a few years before, when not so many people had cell phones, the technique, while still striking and innovative, might not have been their most effective tool, or even effective at all. That is how I saw the sentence, but as you point out RonBee sees it differently. And it's splitting hairs to argue over it anyway; the point the author is making (new technology has empowered grassroots citizen action!) is clear either way.
The important thing was the as/in conflict, which I think we have successfully dealt with, thanks to BobK.
I've learned a lot from this board too; I don't think I've ever spent so much time considering the power of the humble preposition.