My suggestion was to introduce a minimum fee in the Bitcoin system. And it is better to introduce such changes at the protocol level. You claim that the disadvantage is that "Need to change Bitcoin protocol to explicitly disallow transaction low fees". 
Although this is not entirely true. The minimum fee can be entered at the level of miners, without changing the protocol. If, for example, 95% of miners vote for this and activate this mode, then blocks with transactions with a fee less than the established one will be considered invalid by the rest of the miners. But I emphasize that it is better to introduce such changes at the protocol level.
Bitcoin network isn't only about miner, but also node. If Bitcoin community don't agree to the change, it'll fail and we'll see 2 chain. Although this is not entirely true. The minimum fee can be entered at the level of miners, without changing the protocol. If, for example, 95% of miners vote for this and activate this mode, then blocks with transactions with a fee less than the established one will be considered invalid by the rest of the miners. But I emphasize that it is better to introduce such changes at the protocol level.
Quote
1. Miners can still fill blocks with their own transactions (spam from miners). But so far, there is no evidence that this happened in reality.
I think transaction with 0-fee could serve as evidence, even though the goal isn't to attack Bitcoin, but to prevent fees on transaction they actually want to create.In fact, most miners can already set any transaction fee they want. If they want to. And you can't prevent it.
The introduction of a minimum fee does not give them this opportunity. They already have this opportunity.
Quote
3. The community has the ability to react to such an event. Most miners should block the "malicious" miner.
If the majority of miners cannot overcome this phenomenon, then the bitcoin community can replace the miners.
Not realistic, i doubt miners would block malicious miners as long as the block itself follow Bitcoin protocol.If the majority of miners cannot overcome this phenomenon, then the bitcoin community can replace the miners.
Consider the situations:
1. Most miners set a high transaction fee. And they stop taking transactions with a lower fee. Technically, they don't violate protocol. But at the same time they cause inconvenience to users.
2. The system has implemented a minimum fee with adjustment from the block size. Miners start filling blocks to the maximum with useless transactions in order to raise the fee level. Technically, they don't violate protocol. But at the same time they cause inconvenience to users. Increasing the size of the blockchain unnecessarily. Artificially increase the transaction fee.
What is the difference between these situations? Why don't miners do the same as in situation 1? And why would they do as described in situation 2? What is the Bitcoin community's response to the first situation, and what is the response to the second situation?
My answer is this. Miners now have the ability to do malicious actions.The Bitcoin community can adequately respond to such actions of miners. Therefore, miners do not do malicious actions. And they won't.