Question: I have an idea that the seas of a world are red, not blue. However, the world should also be the birthplace of an intelligent alien species. Would it be scientifically possible to have a world with a red sea and where intelligent life can still develop?

Answer: 
Sure. Just have a microorganism endemic to the seas that colours them red. Some sort of algae, maybe, that produces a red dye naturally as part of their life cycle. We kind of have that here on earth, manifesting as a [red tide](https://en.wikipedia.org/wiki/Red_tide) during algal blooms.

If the coloration is produced as part of the normal behaviour of the algae, rather than during oxygen-consuming blooms, you're good to go.
The reason our own ocean is blue is because of the color of the sky. If your sky is red/orange, you might end up with a red ocean. You could also do what a couple others have said and try an alga that's red.