They kidnapped him nearly a month ago. He was kidnapped the same day that man who recently escaped was kidnapped.
That man escaped and they had been holding Nick Berg for a long time (30 days). He was a liabilty and posed a risk (if they were caught with him or if he escaped).
The abuse reports certainly were connected because they mentioned them. How much it politically was involved in their anger (vs how much they knew the press would report that the abuse "angered" the opposition) I just do not know.
Also, the arab press ran front page photos that came from a porn site. This story has received little attention here (although the US Embassy in Cairo asked for a retraction from the Arab press). The Daily Mirror also ran fake photos (of men being urinated on).
Don't know how much it was the fakes created by the left that angered the IslamoNazis.