The correct sentence is "facts and opinions are not necessarily in opposition". That is so because one can agree with a fact.
On the other hand "fact" may not be a synonym of "opinion". In research you can use "facts", "opinions" or both. It is so because one does not exclude the possibility of using the other. They are not necessarily anthonyms/ opponents. an opinion is not more important than a fact, but on the contrary, because facts can be proved easier than opinions.
