V1 sites were dealt with by a completely different branch of the air arm, using ground attack aircraft.
They couldn't even hit them with the strategic bomber fleet, so they went on being infective with that on city sized targets. But to say that campaign was negatively affected by a focus on dealing with the V1s is both wrong and misleading.
"Carl Spaatz, commander of U.S. Strategic Air Forces in Europe (USSTAF), responded on June 28[31] to 'complain that Crossbow was a 'diversion' from the main task of wearing down the Luftwaffe and bombing German industry' for the Combined Bomber Offensive, and to recommend instead that Crossbow be a secondary priority"
Saddam Hussein's Scud missile attacks had the same effect. The US diverted a lot of its resources towards stopping those attacks, despite the Scud being so inaccurate it was militarily useless. (Ironically, the Scud missile is just an upgraded V2.)
The 8th AF was also pressed into bombing those sites, and the RAF also used bunker buster bombs on the concrete ones.
Besides, if you have X manufacturing capacity, if you build lots of bombs and ground attack aircraft to go after V1 sites, you're necessarily building fewer bombs and aircraft for Harris' carpetbombing program. The V1 defenses also diverted many squadrons of fighters on constant alert to shoot them down, and mass quantities of flak guns along the route to London.
Ground attack airplanes being prioritized for V1 launch sites weren't being used to attack other things, like railways, industry, etc.