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:
- it's possible that the gmat does consider such constructions wrong; the only way to tell is to see if they say so in any official answer choices
- 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)