So I've jumped on the Elite bandwagon a lot later than most of you guys, so forgive the rookie unfamiliarity with the lore. But I'd like to think that the relationship between humanity and the Thargoids is the product of one gigantic misunderstanding after another. As in, we got off on the wrong foot from the start, and it just slid downhill from there. I forget what book it was, but I remember reading a science fiction novel where a huge interstellar war was set off because one alien species' idea of a friendly greeting was to approach a ship with their weapons ports open. Same idea here.
So, I bet at one point the Thargoids said, "We get it, don't mess with the primates." They turn inwards to do their own thing, Thargoid stuff, whatever that is. Then we start slowly encroaching into their territory, namely the Pleiades, California Nebula, Witch Head Nebula, etc. So we're in their face again, and they're testing the waters to see what our intentions are. Except we're doing stuff like raiding their mining extractors (barnacles), rummaging around in their bases, and getting into shooting matches with their scouting vessels.
So my idea is that we're making our bed, and we're about to lay in it.