Totally depends on the design of the header. Backpressure is kind of a mis-nomer... People think that because smaller exhaust systems create more low end torque it is because the smaller system creates more pressure in the exhaust system, this is totally completely NOT TRUE. What it does, is harness the momentum of the moving air to create a vacuum in the exhaust system as the valves close, helping to pull more air / fuel into the cylinder. This is why it is SO critical on 2 stroke engines... The exhaust and intake are open at the same time usually so if you don't have the momentum of the exhaust gas to empty the cylinder, what is going to pull more air in?
The exact same principle works on an intake, only in reverse. Using the momentum of the moving air to pull or push more fuel / air into the cylinder. So the real question is... Is the stock exhaust manifold really tuned for low end performance? Does it actually help low end torque? Does anyone have dyno numbers? For the exhaust manifold you are taking off vs.. the header you want to put on?
I'd go for it! I suspect you won't notice much difference on low end torque. I don't think it will effect your fuel mileage much either... but... idk...
Alright, now bring on the nay-sayers!!