obstruction call

[blue]

By your description this sounds like a bam-bam play, everything happened almost at the same time. I don't believe you can have obstruction on the defense. When F5 makes a play on the ball, and misses, he just can't disappear. Realizing this is a HTBT play, and I wasn't there, I think the runner has the responsibility to avoid the fielder who is making a play. In this case, you say the fielder missed the ball without interference from the runner: I think you have a crash, no one's fault.
That being said, if all play had stoppped because of safety concerns, I think it's a good call to call dead ball, and place the runner on 3rd. If everyone is concerned about the safety of both players, and it sounds like they were, I doubt if anyone would complain.