That is one perspective. Considering the closest the penalty came to be enacted was 2 years away and health insurance coverage is changed year to year I'm very skeptical that those penalties were the root of any changes. There is a 500 pound gorilla in the room (cost) that seems much more likely to be why changes were made.
I could see the benefits for a PCP or Dr Office opting out because the insurance contracts and billing are a huge resource burden. You're talking more than 1 full time position per office and the insurance reimbursements are crap anyways. A regular doctor's office could charge $40-$50 per visit and be money ahead vs taking copays and billing insurance.
I've always felt that how we use health insurance in this country is a bit weird when you compare it to other insurances that we're familiar with. Like... our car insurance doesn't cover oil changes and we would think such a plan is ridiculous. For some reason we're covering random Dr visits with health insurance though? Why are we doing all this paperwork for something that is less than $100?