You used the word "democratic" twice. But I don't see what democracy has to do with it. The whole point of a democracy is to allow the majority to bully the minority. The protections you need are Constitutional limitations.
The first question is too subjective in general to have a useful debate. I'll just say that complaints about interference in local affairs have been a mainstay of all political unions ever formed, including The United Kingdom of Great Britain and Northern Ireland. Just ask the Scottish. And it's completely natural because "interference" is just another word for "governing".
However, the parent post was about the democratic legitimacy of the EU commission. The commission is not directly elected just as most other governments are not directly elected. In most countries cabinet ministers are not even elected MPs. Parliaments are elected and sometimes heads of states but rarely governments. The closest thing to an elected government are probably the presidential systems in the US and France.
Most critics of the EU do not want an elected EU president or a directly elected EU commission as that would obviously take away more powers from the nation states. That's a legitimate position, but it's incompatible with criticising the EU for not being democratic enough.