I've used it in secondary before. I made a peach mead once and it had a slight haze that wasn't going away no matter how long I aged it (it was in a carboy had to be close to a year old). I was at my LHBS for some other stuff and asked the guy if he had any thoughts. He gave me some pectic enzyme (it was the liquid form), which I was unfamiliar with at the time. I put some drops in and that mead dropped crystal clear overnight.
I agree with following the instructions and using it pre-fermentation, but if your batch is hazy and you suspect pectin, I would go ahead and give it a try.