It's not as simple as that, with lightning network you basically lock your Bitcoins for a month or whatever time period and within that delay where they're locked you can still move them if you and the supernode both agree to it. What this allows for is to just keep a running total of how much you've spent with that channel and when you spend 0.1btc you give the supernode the transaction to send 0.1btc to them and 0.9 btc to you. As you add payments over the course of a month you resend transactions for your current highest amount spent.

At this point all of those transactions haven't been broadcasted to the network, it's private between you and the lighting node. Normally you need both parties to agree to send a transaction but even if the lightning node is malicious they can't spend any Bitcoins and if they don't broadcast the highest transaction they got from you then at the end of the lock period you can take all of your Bitcoins back.

Basically neither party has to trust each other, the worst that a malicious lightning node could do is make you wait until the channel closes to get your remaining balance back.

Mining pools are also a kind of super node; do they run against the idea of decentralization? Some people say no since mining pools cannot cause much harm and some people say yes but offer no alternative.

If a mining pool doesn't pay out the earnings, it quickly gets abandoned by miners, and stops being a 'super node'.

Yes. You're missing that it increases the value of my BTC investment. I don't really care about centralization - what I care about is making money.