Should I apologize & rekindle the friendship or drop both of them?
I can understand why you feel confused by this situation and their responses to you. First of all, "Ben" was not honest with you when you asked about his relationship status with "Clarissa". You did go to him first and he was not honest.
Knowing this may have been the case, it sounds like you approached "Clarissa" for more of an honest, clear answer and received one. You walked away feeling better about the situation, at peace with their relationship, willing to continue a friendship with both Ben and Clarissa, and made plans to talk with Ben about your meeting with Clarissa.
I am sure you were surprised by the turn of events when you learned they both were upset by your visit with Clarissa. It seems you are aware of an area you want to apologize for, which is hanging out with her to find out about their relationship as the true intention, instead of getting to know her more. If you are feeling led to apologize for this, then it is okay to do so. If you decide to apologize, I encourage you to only apologize in that area alone and not take responsibility for the areas that belong to them.
For instance, you did go to Ben first about the relationship and did not receive an honest answer. Also, you did intend to continue to develop your relationship with both of them after you received Clarissa's honest answer. Clarissa led you to believe she appreciated the visit and felt the same about a friendship developing between both of you. I realize I am on the outside looking in and only see the information put in front of me, yet due to this information, they both seem to struggle with honesty.
You have outlined three plans you are considering. Which one gives you the outcome you most want plus helps you find some peace? How much do you value your relationships with Ben and Clarissa? Given the circumstances, it is hard to determine how they may react to either plan you decide on. You have been placed in a difficult spot by them and they must also choose to be honest with you for a healthier friendship in the future.