The article talks a lot of scare, but if you visit the supplied link to Visa about what you need to do it gets a lot less scary. That makes sense as otherwise huge portions of merchants would be set to lose the ability to take cards and CC companies / gateways would lose buckets of cash.
http://usa.visa.com/merchants/risk_management/cisp_merchants...
Level 3 merchants (up to a million transactions a year) need to complete a self-assessed questionnaire annually, fill out a form and have an automated external test run. All are very minor hurdles and if you're running that many transactions should be an extraordinarily small amount of expense as a percentage of revenue. If you're doing 20,000 transactions there is even less to do.
tl;dr FUD