I really don't think Hurt's doctor's crime is ending the time war because:
- We have already covered that with the End of Time.
- Both the Daleks and the Time Lords were 'bad' and thus are not getting any sympathy from fans when they died.
- The Daleks have come back and the Time Lord can (and almost have) come back to, so therefor there is no real finality in there destruction.
- We have had years of the dealing with the Doctors 'Guilt' already.
The Doctors crime will involve the death of innocents. Perhaps during the Time War the Doctor had to commit genocide of an entire population of innocent beings in order to save the universe. It will be more something on these lines and not ending the Time War.