I have had the same question at some times in the past. I have a hard time reconciling the God of the Old Testament with the God of the New Testament. So I wonder how much of what happened in the Old Testament was REALLY God's direction - or just primative cultures projecting their own decisions/desires onto God.
Anyways - I've done a lot of research and soul searching over the past few years and am now a born again Christian - so I'm putting ALL my $$$ on God's side.
However - SHAME ON ANYONE if you dog someone for asking the question. Never be afraid to ask questions. It was my fear of asking questions that kept me in the JW stronghold for so long. One night while praying I appologized to God for having the questions in my mind (you know - are JW's really God's organization, is he a trinity or not, should I go back, etc) - at that moment a thought came into my mind - it was very clear "Ask your questions. The truth will always be there." Call me crazy - but I knew it was from God, because it was not something I would have ever said, and it was very strong. Immediately the guilt I had carried for so long about these doubts was gone and I started in my research full-force. That was what began my road to freedom.
So ask your questions - whatever they are - and never be afraid of them.