Yes, the attacks stop after the DG MQ.
As to the attacks, they are easilly managed.
1. Never travel to or around in a city/town/settlement after dark. If you have to travel to a city, Save first, then try to time your fast travel so you arrive at daylight. If not, reload, and wait a different period of time or travel to a place near the city, wait until morning and walk to the city. This restriction makes sense, because if there were Vamps out and about, you would avoid nocturnal travel.
Doing this, I never had a town attack during DG. The DG quests tend to keep you away from the cities, so focusing on that will not require much city exposure.
2. If you have to be out and about in the city at night or want to have a Vampire Attack, then wait inside until 6 PM, then again until 8PM, then again until 10PM. This will trigger the NPC commute scripts that tend to bunch up NPCs at the city gates where the attacks occur. Once you have waited until 10PM, those scripts are done and all you have are generic gaurds out and about (for the most part)