Hey there,
"Take literally" is used when you might be ignoring the context of what the person is saying a little, for example if I said "I've had such a stressful day, I just want to jump off a bridge" and you said that you took what I said literally, you'd be saying you thought I was really going to jump off a bridge.
"Take at face value" is like saying that you will take however something seems as how it is, for example if you've watched a trailer for a movie and you thought it looked bad and then assumed the movie is bad, that is an opinion you have taken at face value. In this example you can't really say that your opinion is something you've taken literally which I hope clears up that they aren't necessarily interchangeable.