It's just my guess, but I think Zamenhof wanted to find a compromise between conflicting principles:
- the written form of the roots should be recognisable,
- one letter should unambiguously correspond to one sound.
"Akvo" comes from Latin "aqua". Words such as "aqueduct" are written "акведук" in Russian, "akwedukt" in Polish, and written with "kv" in most other Slavic languages (as well as in Baltic, North Germanic and Finno-Ugric languages, for that matter). "Q" isn't used in Esperanto, so writing it with "qu", as in most Romance and West Germanic languages, wasn't an option anyway. I don't know of any popular languages that use the spelling "akua", "agva" or "akfa", so "kv" is the best choice here, if we want a recognisable word.
The pronunciation is a simple consequence of the "one letter, one sound" principle. But I think some people are unnecessarily taking it to the extreme. The pronunciation "agvo" or "akfo" is not wrong, it's simply not recommended:
En Esperanto gxi povas konduki al miskomprenoj nur en vere malmutaj okazoj (subtaso - suptaso), do eble estu tolerata - sed ne rekomendinda [...] (Wells, J. 1978. Lingvistikaj aspektoj de Esperanto, p. 24)
So, there is really no problem if you pronounce "akvo" as "agvo" or "akfo". If you say a word that somebody is going to write down, using the recommended pronunciation will make it easier. But in the great majority of the cases, it doesn't matter if you make it voiced or not, and most people won't even notice.