Yeah, that's exactly why it wouldn't work in movie-verse. But I don't think there is much need to worry even in the future. SHRA doesn't make sense in either the Movie or the Ult-verse because the premier superhero team in both cases is directly under SHIELD jurisdiction. In that case, independent teams outside the Gov's control seems a hard paradigm to achieve.
But in 616, Tony worked specifically so that the Avengers would *not* be under anyone's jurisdiction. They answered somewhat the Gov at first, but Tony fixed even that with making the Avengers part of the UN (I think briefly they were a sovereign state in themselves, shortly before Disassembled) This made the whole environment, really really friendly to 'lone heroes', people who did not answer to anyone. So of course, perfect ground for the Gov to try and exert control, and hence Civil War.
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But in 616, Tony worked specifically so that the Avengers would *not* be under anyone's jurisdiction. They answered somewhat the Gov at first, but Tony fixed even that with making the Avengers part of the UN (I think briefly they were a sovereign state in themselves, shortly before Disassembled) This made the whole environment, really really friendly to 'lone heroes', people who did not answer to anyone. So of course, perfect ground for the Gov to try and exert control, and hence Civil War.