It was agreed on the EU would not interfere with tax affairs a long time ago, this does exactly that. The exact way it was done is irrelevant, it is the result that is the issue.
In the UK it was said when legislation from the EU was rejected or sent for revision, it would be sent back in another chapter of an irrelevant part of a policy document on another issue. This is what used to anger lawmakers.
The way of getting things done is never through the front door (going at taxes directly), it's always using a backhand trick to get around to managing policy (competition policy), which is quite underhanded.
While it is wonderful that Apple will now be paying taxes, who's to say this power will not be abused by the commission in future?