Dune: The Dice Must Flow!
If I don't want to take the dark pact stated in the research card to get the clue is the clue token discarded? I don't see anything in the rules that deals with this specifically.
When posting a question, it's a good idea to mention the situation your in (on a city space having completed a Research [Clue] Encounter successfully), what card your looking at (all cards are of a type and have a number or title) or quote the EXACT text from the card.
In your case, the Clue stays where it is and can be encountered next round ... hopefully you'll get a better/easier Research Encounter!