The reference by Josephus was a later addition to his writings by a Christian forger. This has been proven by comparing Josephus' writing style with the obviously anachronistic grammar used by the forger in the early copies where the forgery occurred. The earliest copies do not include the reference to Jesus. In addition the reference is out of place with respect to the narrative and was obviously inserted without much thought.
The problem for these other theory's is the Roman soldiers would have been killed themselves if Jesus would have been let off the cross alive, therefore they thrust a spear into His side to insure death. This also had to be done to fullfil several prophecies. They pierced Him, He was dead, no doubt about that. He was seen walking around for 40 days after His resurection by many. You also must remember He had been beaten so much that it marred His visage, according to Isaiah, so some may not have recognised Him right away. The Bible has proven to me to be trustworthy and historicaly true. To my knowledge, it has never been proven wrong.
If you keep your eye on the big picture, Jesus was sent here to die and purchase His Bride. The miracles, The speeches, and all the extras were just to fullfil prophesy and prove who He was. We either accept His gift or not. A human heart is dark beyond explaination. I believe Jesus could come and preach at any church today in the flesh and some would throw Him out. My job is to testify, the Holy Spirit brings belief. Without the Holy Spirit, a person can't belive even with the proof right in front of them.