The content was subject to a large amount of wordfilters at the time, which would alter half the posts.

...but those were public. It's one thing to have a computer run search and replace on every post in the board. It's quite another to have a mod specifically edit your post, making it look like you said something you didn't.

I've been wondering about exactly that - would the perception of this be so negative if spez had inserted javascript to rewrite the messages on that subreddit instead?

No, because that would rewrite everybody's messages. And it would be noticed immediately, so it wouldn't even matter, practically.