Because they provided the technology that Scott used during CA:CW. Aiding people who violate the Sokovia Accords is a violation of the Sokovia Accords. There's a chance they could have prevailed in court (Scott stole the suit) but as mentioned above, they didn't trust the system. And Scott didn't act like he was dragged to Germany against his will; I don't know why "dragooned" is the default setting over "volunteered."
I'm in the camp of liking the smaller scale movies just fine; not everyone has to save the world. And it helps with Marvel's long-running third act issue. Most of the time, the third act is a big action spectacle, but the action doesn't have much suspense. Will the Avengers defeat the alien invasion? Of course they will. I think CA:TWS had a third act that finally had real suspense. Not whether Team Cap would save humanity from Project Insight (of course they will) but whether Cap would have to kill his newly-rediscovered best friend to do it. Here, the third act had more options than just victory or (unthinkable) failure. Granted, I was pretty sure that Janet would make it back and she'd be able to fix Ava, but that was a conclusion I came to during the third act, not right before it started.
The other thing about scaling down the villain threat is that they're already dealing with something big and scary: the Quantum Realm. They could have made that the villain, and I would have been just fine with it.
I had a good time, and I look forward to seeing it again.