See, I don't think the Jedi needed to involve themselves with the army. The Republic pretty much did, it was take it or be steamrolled. But there wasn't any reason for the Jedi to command them, especially given the incredibly suspicious nature of it all from even preliminary investigation.
Oh, also, Infernally Clay, I did not see the Jedi being explicitly antagonistic towards Anakin. I asked earlier, got no answer, so I'll ask again. Please, detail that for me. They take him in as an older student. They pair him with a great Jedi. They treat him as they do other Jedi. Hell, they even let him go on a cushy protective service to Space Italy with a friend from his childhood! Those damned Jedi, always keeping Anakin down!