Of course the episode is fine for family audiences. There are only two things in the episode that are at all iffy, and when you think about it, even they aren't really bad:
1) The sub (Mr. Bergstrom) makes jokes about his own name, suggesting that the kids should call him "Mr. Nerdstrom" or "Mr. Boogerstrom". What makes it not bad is that it's a good way for a sub to break the ice with a roomful of strange kids, and it happens in real life. In high school Spanish class, I once had a substiute teacher whose last name was "Godbold", and as soon as he introduced himself he said that he had heard all the jokes there were about his name, and therefore any that we came up with wouldn't bother him, and then he made a pun or two himself on his own name. It WAS a good icebreaker, and the fact that I still remember it 30+ years later shows that it made an impact.
2) The only other iffy thing is that the plot revolves around Lisa developing a schoolgirl crush on Mr. Bergstrom. But again, it isn't really so bad, as it makes for a tender, heartwarming story and it also happens often enough in real life!
So, you're not the only one to have noticed that "Lisa's Substitute" is perfectly suitable for family audiences, and that does indeed make it stand out among the body of Simpsons episodes.