IMO I don't think the State HAVE sufficient evidence to discredit OP's claim that he thought there was an intruder. At the risk of "sounding like a cracked record" I think they should have from the outset argued the case accepting that OP THOUGHT he was firing at an intruder. The State have spent 2 and a half weeks (excluding late starts, early tea breaks and early day ends) trying to prove Beyond Reasonable doubt something that they can not prove at all. They knew what evidence they had. We have seen that it largely supports OP's version of events.
Correct me if I am wrong, but as far as I recall the prosecution has not at any time disputed OP's claim that he thought he was shooting at a burglar merely put forward evidence for the defence to chew on. The State's charging document makes no mention of "premeditation" rather the "unlawful" and "intentional" killing of a person, i.e. Reeva, which seems correct according to SA laws.
IMO the verdict will rely on whether OP could lawfully fire at a perceived intruder. The fact he killed Reeva by mistake seems to me irrelevant in the scheme of things. It would be like a hired hitman killing the wrong target by mistake. Would the hit-man then be found innocent of murder simply because he made a mistake in the the identity of the person he was meant to kill? I am sure not, which is why IMO the verdict will rest on whether OP could "lawfully"shoot at a perceived intruder, and whether he intended to kill the perceived intruder or even if he didn't intend to kill the perceived intruder should he have known that his actions could kill the intruder. As far as I can see the fact he shot and killed Reeva by mistake may sadly be just a sideline.