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.
If the oceans contain very high concentrations of iron, in the form of rust, it would create a red ocean. 

This environment would be ideal for [rust-eating microbes](http://www.nbcnews.com/id/40533835/ns/technology_and_science-science/t/new-species-rust-eating-bacteria-destroying-titanic/), which could form the base of oceanic food web in the same way photosynthetic plankton form the basis of our aquatic food webs. 

What implications this has on your world's plant and animal life is outside the reach of my familiarity with biology, but I don't think it would necessarily preclude the development of intelligent lifeforms.