Actually some forms of inoculation have been around for millennia - the Qu'ran may well warn against some of the cruder, more dangerous forms.
Chicken pox parties are a form of rudimentary inoculation - the idea being that children get the illness when they are young and in a relatively low risk group, so that they don't get it when they are older and it would be more severe.
In any case such a warning is not really relevant today.
Encephalitis is generally one of the (very rare) reactions listed on vaccine info sheets. I know it was one that scared the shit out of me when DS1 was tiny. I'd never had any idea vaccines could have such side effects. I did know that it was a side effect of (e.g.) Measles, too, but my thinking was that he'd have to come into contact with an infected person (probably not that likely), then contract measles (doesn't happen to every contact), then have a particularly severe case (not very likely) - it seemed like a remote risk and yet having the vaccine was a definite risk, no matter how low. Also the antivax sources I was reading seemed to suggest that the vaccine reactions were many times more likely than they actually are.
I also didn't really know very much about disease transmission when I was having that panic moment - my experience was limited to things like colds and chicken pox and so on - so I thought even if you had contact with a sick person, it wasn't that likely you'd catch something, just moderately. Thanks to covid I think a lot more info has been made accessible about disease transmission rates - sounds silly, but I didn't really know that they varied, I just thought something was either infectious or it was not. Anyway Measles in particular is one of the most infectious diseases in the world, you need a very high rate of immunity to keep it at bay. So it's a no brainer really to have a measles vaccine, because without vaccines most people would definitely get it, and when you compare the numeric risks of the vaccine with the risks of the disease, the vaccine wins substantially.
When DS1 was tiny when I finally decided I would get him vaccinated, I was fully under the impression that I was making a choice which was just about as risky as the alternative, and actually my main motivator towards going with vaccination was that it was the norm, so it was what doctors and other medical professionals were used to and experienced in dealing with.