Dear hupay problem is that Ebay never followed any law in the first place. There is general rule of e-commerce selling in India that unless you are selling exempted category items, VAT is mandatory. Other sites like Amazon and Flipkart don't let anyone sell without VAT. But ebay disregard this rule for years. That's part of the problem.
As for latest govt relaxation, problem is that how will e-commerce site determine that a seller has less than 20 Lakh turnover. They will certainly won't go by verbal assurance of the seller.
In most likelihood they will ask the seller to get it in written from bank. This in itself won't be easy especially for sellers who are using savings accounts for e-commerce transactions.