Stop words are used by Indexer while creating index. It is not something that happens on the fly. So I don't think what you are thinking is possible.
In this case you will have to create two indexes using appropriate Stop Words and then call that Index appropriately.
What you can do alternatively is to construct your query dynamically. Let's say you want to ignore stop words of englidh language like "a", "an", "the". SO before sending your query to the index you need to remove these words appearing as a part of your query. This way you will never search on these stop words.
You can extend this language to dynamically remove stop words as per language also.
Let me know if you need some code to remove stopwords.