Do not use redirection characters in your shell prompt

If you could configure the common shells (bash, zsh, fish) to run a custom command on submitted shell input before executing, you could build a heuristic function that would attempt to recognize when you were pasting in a prompt. Unfortunately, I'm not aware of such a capability, as it would be useful in a number of situations.

Another alternative is to put the octothorpe # at the beginning of your prompt - then you can keep your > at the end.

I recall terminals (MacOS Terminal? definitely Konsole seems to) that prevent any paste from actually executing the command, even if it contains newlines. Doesn't that solve this problem?

Fish just doesn't seem to process the redirected output to clobber the file when a command isn't found. If your prompt is a valid command it can clobber a binary but not otherwise, apparently.