I suspect that the only way to effectively mitigate this is in the terminal application, by displaying a confirmation with the pasted text before accepting any multi-line[1] paste. For example here: https://code.google.com/p/iterm2/issues/detail?id=594

[1] There may be other dangerous characters besides newlines, e.g. escape sequences. I'm not sure if it's possible to make an exhaustive list for something like Bash. Perhaps one has to guard against any paste?