This is nothing new.
Jean-Claude Juncker, the previous President of the European Commission, famously said that "There can be no democratic choice against the European treaties" (he was referring to the possibility of Greeks voting to reject the MoU with the Troika; they did, and were promptly overruled).
Going further back, when in 2005 the European Constitution drafted by the Giscard D'Estaing working group was rejected in referendums by France and The Netherlands, it was simply renamed as a Treaty and approved basically unchanged in Lisbon in 2007. As it was now a Treaty, not a Constitution, no popular vote was deemed necessary.
In general, EU institutions are inherently undemocratic. The two main law-making bodies are the European Court of Justice, whose pronouncements would require a unanimous change in the Treaties to be challenged (as such, it has even more power than the US Supreme Court, for example), and the European Council, where each country has one vote; hence Estonia, who has a smaller population than Milan, counts the same as the whole of France.
And the least be said about the 'financial waterboarding' powers of the ECB, the better.
IPB