I didn't filter my water. The Annapurna Circuit development council guys have built community-run water stations in several of the villages, so you can buy a clean liter of water for very little, about 50 cents I think. When there wasn't a water station nearby I just used chlorine tablets and then added the taste-remover tablets to make it palatable. I wasn't so keen on drinking chlorine for 3 weeks but I didn't suffer for it.
As for the road at the start of the circuit, it only continues for a couple hours past Besi Sahar, just up to where I slept the first night, Khudi. This is where the jeeps unload their goods onto mules, I believe. Unfortunately the (over)development committee seems intent on putting a new road in, following the trail across the valley. Road teams were blasting when I was there, and the military made us wait for an hour before it was safe to go ahead. At present the trail near the beginning alternates between a narrow village-linking trail and a road that can handle mule traffic more easily.
Once the valley opens up around day 5 there's a lot less construction and more untampered wilderness, but it is important to remember that these are not pristine nature trails, but miniroads that have connected towns and regions for hundreds of years. Meeting people and their yaks is part of the experience. Other than the blasting on one day, I didn't really find these mule-roads all that distracting from the awesome mountains.
The trail on the west side, however, is another matter. Someone mentioned that it is possible to avoid the road with a good guide, but unfortunately the dust that the buses kick up makes the mountain views a little less spectacular, and you can hear them honking for miles and miles. I walked the west side just to see what it was like, and it is certainly still a world-class place to see mountains, but the first half of the circuit is much nicer.