I think that in my reply I may echo some of the sentiment expressed by Gauracandra so forgive me if I do.
Using the analogy of a tree will only get us so far, the tree may be perfect but in one year the yeild may be attacked by bugs or frost etc. Some of the fruit will overcome this and go on to ripen fully, these are the fruits we should judge it by.
A fault with your thinking is that the fruit from a tree is not concious (as we are) and thus does not represent how our desires and conditioning may carry us away. The guru can only do so much, it is ultimately up to the disciple to carry out the instructions that the guru has given him, he cannot be expected to live the discple's life for him.
We should, as I said, judge the tree by its best fruit and I can only assume that you have not yet seen all of the fruit from the Prabhupada tree.
Please do not be disheartened that you have these doubts and questions, if you are sincere then Krsna will reciprocate with that sincerity and send you a worthy guide, until then you could check into the dailysanga.com website and see how one of Prabhupada's disciples has fully ripened and is bearing fruit of his own.
in service
DayalGovinda dasa