If you're going to stretch, that's the way to do it.
The thing about running and most aerobic activities is there isn't a lot of sudden movement which risks injury - the best way to warm up for the activity is to start into it at an easy pace and speed up as you warm up. Weight lifting OTOH (and my other sports, kendo and judo) have opportunities for injury. With those, it's definitely do something aerobic to break a light sweat, then stretch out.
My advice comes from a friend who's a fairly serious triathlete. He says about 90% of running injuries are caused by overstretching. I'd say that's stretching the point a little as many runners get non-stretching related injuries. Still... the only injuries I get from running have been soreness in the knees, and that's just an overreaching thing - my 43 year old knees need time to adapt to increased distances.
Other runners do run lightly for a few minutes, then stretch, then continue. I don't think it's necessary.
The post-activity stretch is what I need for running - if I don't, I can get some cramping, especially in my calves. Running tends to tighten up hams and calves.
I've got good advice there - Keith Hobman, misc.fitness.weights resident guru, lives in my city and has helped me with my program and general approach.