B) you can't use 'that' in this sort of construction, because constructions using 'that of' (or other preposition after 'that') must have EXACTLY parallel structures. in other words, if the second half says 'that during 10,000 years', then the preceding half must say 'the growth of ___ during something else' (or some other time preposition, such as before or after, in place of during).

there's nothing ungrammatical about 'from when', because the clause starting with 'when' is a perfectly legitimate noun clause (i.e., 'when agriculture began' serves as a noun. however:
- regardless of where the gmat stands on the issue, 'the beginning of agriculture' is unquestionably better than 'when agriculture began' (i.e., an actual noun is almost always superior to a circuitous noun clause, when possible)

C) first, you've got a "which" modifier that isn't preceded by a comma, so that's an automatic failure. (note that you can use preposition + which without a comma -- e.g., the box in which you placed your valuables -- but you cannot do so with just plain "which".)
more importantly, "had been" is not parallel to anything in the other half of the sentence; in order to use a parallel structure that contains a form of "to be", you must have another form of "to be" in the other half of the parallel structure.

D) you can't use the present perfect if the time interval is over. If the trend continues into the present day, then the present perfect is appropriate.
Even if that were fixed, choice D still suffers from fatal wordiness / lack of concision, especially in comparison to the correct choice."

E) 'what it did' doesn't make any sense:
* the growth didn't 'do' anything
* there's no other verb to which 'did' could logically be parallel to complete the comparison