gsark,
Actually, their actions make perfect sense if you don't think they were divinely directed. The Isrealites killed off all of the adults because that's what warring tribes did in those days - and of course you didn't want any sons left alive because they might grow up to try to take vengeance against the slaughter of their parents. Girls, on the other hand, girls were useful. You could always use an extra concubine or subjugated worker.
And as for killing off the women to avoid venereal disease... I would tend to think these diseases are not so rampant as you would think, else how would the other tribes have survived long enough for the Israelites to conquer them? I think it is more likely a result of a cultural fixation on virginity, plus the practical realization that young girls are easier to assimilate than grown women.
The only place God necessarily comes in here is in justification for why the Israelites had to slaughter everyone in the first place.
Just my thoughts.
-T.