I wish I was wrong about that, but I’m not, since you’re right! (?!?!)
The Gardens of Equestria are a combination of science and magic, and thus ran what was essentially an arcane computer program. Although fusion and fission are distinctly different, and as you pointed out, ideal fuel is NOT inherently radioactive, both processes are still considered nuclear reactions and thus were nulled. And as anyone who’s ever operated a computer can tell you, programs lack any sort of sense and only do what they’re told, so ‘exceptions’ for such things weren’t programmed into it for whatever reason. Perhaps due to a lack of time, or mere oversight? That doesn’t sound like Twilight Sparkle or the Ministry, though..
Alternately, fusion reactors may have been included intentionally, since the designers may have feared some sort of weapon or power source which we haven’t even come up with yet. The only ones who know for sure are those whom built it, and they’ve been dead for centuries. No ghouls who may have been in a position to know have come forward in the last decade, either.
It could also have to do with the megaspells the zebras were known to have; perhaps their process is similar to fusion? This is one question I truly cannot answer with anything other than theory, as the truth is buried in the flow of time.
(Excellent question though, Anon! And yes, fusion is a hell of a lot safer then fission and you can’t get runaway reactions or meltdowns or all the other awful problems you get with standard nuclear power. But, for story purposes, it too was negated, along with virtually all magic and technology related to ionizing radiation.)