Doesn’t really matter...
They did, in Avengers. Or, if you’re talking exclusively about Symbiotes, it’s not like people are really sure that Venom exists. For all the public knows, some bad guy company just did some bad stuff to people, stuff no one would want to even know about. Besides, S.H.I.E.L.D could easily have been off-screen at the end, they never showed what happened.
Same thing here.
Really, it’s not that massive of a deal. It was a small feud of a climax, something that would beg similar questions from Iron Man 3 and Captain America 2 and nearly all the solo films. Would it have had disastrous consequences? Maybe, but it doesn’t really feel like something they’d need to intervene with.
Your points are valid, for sure, but I think the larger problem would be Disney and Sony’s reluctance to co-work on projects.