IMHO it is hard to say what might have happened if the Soviets (and or the Cubans) had put more effort into camouflage and deception as my understanding is the US had a certain amount of human intelligence available and they were also prepared to fly very low level reconnaissance sorties over sites of interest.
Low-level sorties might work, yes. What's your understanding of the amount of HUMINT the US had?
In my view it is hard to say how conventional strikes against the Sam sites might have played out in that context. If the point of the strikes against the sam sites was simply to destroy the sam sites in retaliation for something the other side did or perhaps in order to send a message, vs suppress them so other targets could be hit the US might have put a lot of effort into destroying the sam sites and might have continued to strike them until they were certain they were in fact destroyed.
The US threw a lot into smashing SAM sites during Rolling Thunder as well, to little success. When the US lost it's first aircraft to a SAM in Vietnam on July 24th, it responded three days later by throwing over 100 aircraft in an attack on two SAM sites believed to be responsible. It was a disaster: coming in low to stay under the SA-2s 2,000 foot ceiling the attackers ran into a wall of flak. Six F-105s were lost for nothing, the SA-2s remained operational and undamaged. Another strike on 9 August by a much smaller force of 12 F-105s on a different site went a bit better: Coming from multiple directions to confuse the gunners, none of the Thunderchiefs were lost and the squadron leader, Major Hosmer was awarded the Silver Star. But once again no lasting damage was inflicted.
The Navy was the first to respond with an all-out campaign, declaring the "Iron Hand" SAM hunting program, which was made public in an attempt to intimidate the Communists. Hanoi laughed in their faces, shooting down an A-4 with an SA-2 on 12 August. The Navy launched a massive hunt for the offending SAMs with its new Iron Hand squadrons. Again, the attempt was a failure, with five more Navy aircraft shot down over the next two days, and no SAM sites destroyed. It wasn't until
October - almost three months after the first SAM efforts - that American BDA declared a SEAD strike that month had managed to "kill" it's first SAM site (so far, the North Vietnamese remain silent on whether the call was accurate). By that point, the American air forces had been so heavily focused on SAM hunting that it deliriously affected their efforts against other targets.
It's worth remembering that the SA-2 was not a new system when it showed up in Vietnam, yet the US Air Force STILL had not properly prepared to face it outside of a nuclear scenario. In fact, the USAF had actually been
better at neutralizing enemy air defenses in WWII, with several dedicated squadrons, but these had been disbanded by Vietnam on the perception that they wouldn't matter during a nuclear war. Historian Craig Hannah called the USAFs failure to plan for, and respond effectively to, the North Vietnamese SAM threat "an inexcusable act of negligence."
The political interference from Washington in the execution of Rolling Thunder is well known, and sometimes blamed wholesale for the campaign's failure, but it was really only a smaller part of the problem. The bigger part was because - at a fundamental level - the USAF of the 50's and 60's had forgotten how to wage a conventional tactical air war, and had developed neither the mindset, nor the men, nor the machines to do so effectively. It's conception of an independent offensive air campaign was no longer to lay down a blanket that attrits away the enemy forces and smothers his defenses, but to deliver a series of sharp penetration raids. Probably sensible enough when you're delivering nukes, but not conducive to taking them out with HE dumb bombs.