In general allowing content to be supplied in advance on stdin is desirable behavior, because it allows a developer to (for example) write applications that work as pipes that can have content queued on the input stream ready for processing.
If that behaviour doesn’t suit your use case and you need to only accept input after a certain point, you could read() and simply ignore/discard the current content of stdin before you write your question/accept the answer from the user.
I’m sure there are ways to suppress output from stdin presenting in the terminal but I couldn’t tell you how to do it without looking it up myself.
The easiest entry point to this problem that I can think of off the top of my head is password input masking (e.g., when you run sudo and type your password, it prevents character output even though the characters are read by the application).
There is almost certainly a much better and more appropriate mechanism to prevent stdin characters from printing directly to the terminal (perhaps some kind of special character? A TTY control option?) but I don’t know it off-hand.