#gram-staining

Yes it is actually very easy to mistake C. botulium for C. tetani because they both have terminal spores. They are also both gram positive bacilli. 

The thing is - after so many years, the bacteria would have died and the only thing Sherlock can see under the microscope would be the spores. He wouldn't be able to tell the difference between C.botulium spores and C.tetani spores under a light microscope. 

I assume that from the post-mortem report there were no signs of tetany. If C. tetani had been used to kill Carl there would be tell tale signs of contortion of his muscles even after death. When they pulled him out of the pool, he must have been floppy as a rag, which is why the conclusion was seizure rather than foul play. 

Also he shouldn't have been killed by C.tetani because all school children are vaccinated against diptheria, tetanus and polio. The immune response I think is to the tetanus toxin and the actual bacteria. 

Botulium toxin may take some time to affect the whole body if directly introduced into the blood stream. When it was only affecting one part of Carl's body he would have been flailing in the water but then as it affect all his limbs - it would have looked like he'd drowned (he did drown very soon afterwards).

In the post-mortem and the toxicology report, if they weren't looking specifically for botulium, they wouldn't find any traces of it. However I'm not sure how long it takes for the effects of botulism to wear off in a corpse but surely the pathologist must have noticed when Carl's body didn't go into rigor mortis. I suppose keeping the body in the fridge would delay onset of rigor and perhaps he was just really swiftly buried. 

I actually don't know if you could introduce enough botulium toxin into Carl's body via the cracks in his skin. It's not directly into his blood stream either so some of it might just be washed off in the water. 

But you make a good point - I think Sherlock must have seen the spores and decided to rule out C.tetani because the facts don't fit.