Is there a point to keeping them alive and in a hidden prison?
Good question. Despite killing the bad guy in the last episode (probably showing, that even with questionable goals and allegiances, he has a heart), he was very insistent earlier on catching their targets alive, there must be a reason for that.
Maybe so all the prisoners can be sent back to the 1960's at once without any memory of being in 2012?
Then they'll all age naturally the next time 2012 rolls around for them. Then they won't be much of a threat