The crux of the argument comes down to the following questions:
1) Is it morally right, or can it ever by morally right, for God to kill people?
(If not, then everything else is moot.)
2) Can God "deputize" people, either individually, corporately, or within a recognized "group", to do such killing on his behalf?
3) Was this a "one-time-only" license, a general license forever to that group, or a limited license for a particular epoch and geographical area?
4) Even IF all of the above are in principle true, does this mean the stories in the OT are legitimate instances of it, or were the people involved rationalizing their conquests either at the time or after the fact?
5) How does one tell the difference between rationalization and God "really telling you"?
6) If God *did* order it then, how do we distinguish (for contemporary use against 9-11 types) when people are making up such a claim now?
For the most part, if not all, this is a fair and reasonable summerisation of the entire argument. The highlighted points are the major issues of contention, and they thoroughly contradict the Golden Rule.