Then I remembered that shell-mode has a very similar problem, where pressing Return at some random point in the buffer will try to execute all of the following contents as a command! I might eventually try to mitigate this with some elisp, but my TODO list is already getting long ;)
PS: I actually use this multi-line input feature a lot, since it lets the command history store multiple lines together. For example, if I'm in some REPL, I'll often enter two lines at once: first to reload/refresh the inputs (e.g. `:r` in nix-repl, ghci, etc.) and second is the actual line of code I want to evaluate. That way, when I get the previous command by pressing C-up I get both lines, which ensures my expressions are always being evaluated in a clean, up-to-date environment. (Note that previous command is C-up, since up on its own will navigate around the buffer!)