Hola Emanuel

Yes, you can use "o" although it would be a slightly different sentence:

You can say: 

¿Prefieres agua o té? 

Do you prefer water or tea?

This is as if we omitted the verb in the second part:

Do you prefer water or [do you prefer] tea?

Using "a" as in the lesson is the same as if you said in English:

Do you prefer this to that?

Do you prefer water to tea?

Prefieres agua a té?

This reflects more choosing one thing over another.

But both structures are pretty much meaning the same.

Saludos

Inma