Maybe they're just taking the whole plot idea from the Earth X/Paradise X stuff, where the Norse gods were actually just highly evolved aliens and not really supernatural beings.
Plus, to me, the whole reason the clone was half cyborg was an explanation that it was too hard to make a complete clone. They had to fill in the gaps with technology. Add to that is the thought that Reed's possibly been working on the problem for years, and a cyborg is the best he could do.
(Maybe this also settles once and for all who is superior between Thor and Kal-El.)