How can I legally land VFR in class D airspace with low and few clouds?
What is the appropriate way to handle this situation as a pilot?
  


First, tell tower about the problem.  They may be able to assign you a different runway, have you loiter (circle) for a minute or three, etc.  It's likely not the first time this has ever happened.

If necessary ask the tower for a Special VFR clearance.  That changes your cloud clearance requirements dramatically in your favor.  Note that the tower is not allowed to offer this clearance to you - you have to explicitly ask for it.


  
  I'm calling up tower before I have a visual on the airport (which would be the case in this situation) would they likely deny clearance to land due to knowing that a singular cloud sits out there and would cause a bust the visual flight rules or might they clear me without regard to the rules?
  


J. Hougaard answered this part in the comments - the tower is likely not checking how far you are from a single cloud.