Good terminal emulators (xterm, urxvt, iTerm2, etc.) have support for "bracketed paste mode" which can be used to fix this problem in zsh: https://github.com/robbyrussell/oh-my-zsh/pull/1698 (original code: http://www.zsh.org/mla/users/2011/msg00367.html)

It's probably easy to write a similar fix for bash.