Is it random? Does your presence/alertness bar have any impact on whether Templars will try to dismantle the zipline?
I've seen these guys all over, generally in zones still controlled by the Templars. It never occurred to me that they were trying to dismantle the ziplines - they just seemed to be working on them in some way. It made sense in my head since these Templars always seemed to be working on the tops of ziplines while regular guards always seemed to be stationed at the bottoms of ziplines (so that I could assassinate them more conveniently).
To answer your question, I imagine that when Templars control a zone, they know Assassins might try to gain access via zipline, so they try to destroy it. But as far as I know they never get far enough to actually disable a zipline. I think it's just a visual cue to let you know that you're in a Templar-ridden area and that they want to disable your ability to move around.