I agree with you. It's a safe assumption that they will not find any method or have the capability to manipulate Bitcoin. Therefore, they can only ever manipulate L2 technologies. This is also why I don't plan on owning any alt coins ever for any serious reason. There's always a human in the loop.

I'm still new to all this and actively learning... but so far Lightning does make sense to me to make transactions faster and more efficient. However, if it becomes compromised to that same level you describe, with the state wanting to know everything you do financially, would there be any reason to keep using it? Does it provide something to Bitcoin that's crucial enough that people wouldn't seek a more secure alternative with more privacy? 

 Options and futures on Bitcoin will be the manipulation of choice. Just like gold, silver and all other commodities.  

 And what would be the counter to that manipulation? Just simply opting out of participating?