Sooo... after joining the storm cloaks the feelings a certain "clan" had towards me turned sour. I killed one of the clan members, shortly after while on the road a band of hired thugs kill my horse. After I fight the thugs off I loot one of them and I find a letter, a contract actually ordering my murder, its signed by the mother of the clan. I then go back to exact revenge for my horse on the mother. Everyone is home however so I end up killing nearly all of the clan members. Will this affect my ability to progress in the future? Will people come to replace the dead family members?

If they died, they're dead forever. Most important NPCs don't die though. A feature I'm not very fond of. Personally, as an extremely powerful Stormcloak Warrior I'd like to just waltz around Legion camps / cities and slaughter everybody, but half of them won't die.

There is an easy way to enable killing everyone.

Add this in your skyrim.ini:

[GamePlay]
bEssentialTakeNoDamage=0

if you have no witnesses , you are probably scott free.