So it sounds like you only used your friend to leverage his money. If that's the case, pay him back his 50% with 10% interest and be done with it. Just explain to him that there's going to be a shit ton of work and you feel it's best to just pay his money back with interest. Take him out for a beer and life go's on.
This would be the easiest solution by far. (Since you have already done this. Otherwise, like others have suggested, DON'T do business with friends or family!! Things DO get uncomfortable in these arrangements.)
On the other hand, if your friend is wanting to get into the business or you think that you might be needing his money or skills in the future you can modify this a bit.
Pay him back his 50% for the purchase price of the site and offer him say 5 or 10% of the site profits in perpetuity or for a set period of time. Be sure he understands that "profits" are AFTER all expenses. (Which includes the value of your time on the site to keep it up & running.)
This way he feels that he helped you and got his money back with a continuing bonus. Check into "Silent Partner" arrangements if this might be more than a one time situation.
If you are starting a site that could rival say Amazon, then you have some serious thought to put into this.
If it is just an Affiliate site to add to your stable you can afford to be more flexible with it.
It's really tough to give you good & accurate advise without knowing all the details. Such as, how close a friend is he? What is his personality like? (Laid back or a little high strung?) What is the future of the site? Was this a one time thing? Are you looking for a business partner?
You get the idea.
Glad you were able to purchase the site & hopefully you get this sorted out in an equitable way that keeps you two close.