As someone who believes in God and The Bible, but not in any organized religion, I must agree with Emperor Jargo. Religion is a way of exploiting the weak and keeping the masses ignorant.
Qui-Gonn used the midichlorian theory to manipulate Anakin, and to eventually get his way. He believed in the prophecy of the "Chosen One" so strongly that he put everything on the line, including other people's possessions (the Queen's Starship) and the fate of an entire planet (Naboo). Decisions he had no right to take upon himself.
Hopefully, Ep2 and 3 will shed some more light onto the whole midichlorian thing, I'd still like to believe that GL didn't just throw them in there to resolve a minor plot point. So FOR NOW I'm giving GL the benefit of the doubt. If after watching Ep3 he hasn't come up with a reasonable solution then I will be happy to join in the midichlorian-hate-debate.