Williams, a devout Muslim, appeared for the Auckland Blues last weekend with the Bank of New Zealand (BNZ) logo on his shirt collar blocked out by tape.
It later emerged that he was exercising a "conscientious objection" clause in his contract, telling NZR he did not want to wear the logos of banks, alcohol brands or gambling sponsors.
His action sparked furious debate in New Zealand, with Prime Minister Bill English saying he did not understand why Williams should get special treatment.
"I sort of understand the vitriol that's happening around the country, people on Facebook and that," NZR general manager of rugby Neil Sorensen told Radio Sport.
He said there was ignorance in New Zealand about Islamic law – which objects to banks earning high interest from loans – and it was natural for people to react negatively to something they did not understand.
But Sorensen said views changed over time, pointing to modern attitudes to homosexuality.
"I remember 20 years ago when I was a young 20-year-old, homosexuality for me was like 'yuk' and it was easy for me to say 'you gay w*nker'," he said.
"But I've learned over the years and I'm a hell of a lot more open and more tolerant now."
Williams' logo cover-up took NZR by surprise but after discussions this week it agreed he could wear a special Blues jersey with no branding from BNZ or Investec, Super Rugby's main sponsor.
Sorensen said Williams had no problem wearing the logo of AIG, the All Blacks' shirt sponsor, which is primarily an insurance company but also has a huge mortgage portfolio earning market interest rates.
But he said the player would not take part in off-field AIG promotions, saying "you'd have to ask Sonny" when pressed on details about his stance.
Sorensen launched a spirited defence of Williams, who has often proved a polarising figure for fans.
"He doesn't abuse alcohol, he doesn't do drugs, he doesn't beat women, he's just a good bloke, you know?
"If we have more Sonny Bills in the world we might have more challenges about different beliefs, but I think our society would be better off."