It's the large overvoltages that kill the ECU- 'spikes'. As long as you don't drag the charger leads over the battery and arc it out, then you should be ok. Same with jumping the bike (and that's how the ECU's were ususally blown). Putting one of these on your bike is completely analagous to putting a surge protector on your computer.
Re: The charging system- When just running the bike, it should definitely not be putting out lots of hash, spikes or elsewise.
Re: fuses- yes they are very slow. An electrical spike can last a few thousanth's of a second (or less) and that's plenty to damage sensitive equipment. A fuse takes hundreds of thousanth's of a second to blow. A transil diode takes a few millionths of second to kick in- much faster- thus saving critical stuff downfield.
You can put a protective circuit in you bike- won't hurt it a bit. Or you can leave it out and trust the engineers to have taken care of it.
All that said, I've thought about making one for my bike- just for fun really. Let me look into the costs and maybe we can do a group buy.
As always, my advice is worth what you paid for it.