The argument is that the deal that Apple brokered would not have been available to any other company.
A country regulating an industry's tax across the whole industry, affecting every player equally, is very different to a sweetheart deal with one company that puts other players in that same market, both at home and abroad, at a grave disadvantage.
The modern EU is based on freedom of access to market and equality of opportunity. This is what is enshrined in the treaty currently enforced. The EU is not forcing "its members to give up tax policy", it is forcing its members to treat companies fairly across the bloc according to those policies which they have each set. Whilst this could be seen as an assault on their sovereignty, for a collective union to work there has to be common rules, and everyone has to play by them; thereby fairness is ensured. Everybody concedes an equal amount of their sovereignty for the common good (c.f. the ECJ). When one country doesn't play by the rules for its own gain, the others are disadvantaged, and so it is only fair that the central body of that union enforces the previously-agreed rules.