No, again I said that the difference is tone, risk and scale. Are the skeletons attacking a village? That's fine by me. Is it a few skeletons hanging around a dungeon? Meh. Are the rats overrunning a farmhouse and there's a little girl in the 2nd story window unable to escape as hundreds of rats swarm up the stairs? That's great. Are they just in a dungeon chewing on food and attacking when disturbed? Meh.BTW I find the quote in the OP that saving a village from skeletons is 'not heroic' and unworthy of starting PCs to be pretty weird! I didn't watch Jason & the Argonauts fighting living skeletons to gain the Golden Fleece and think "Newbie Fetch-Quest, how dull!" I didn't watch "The Magnificent Seven" and think "They're fighting to protect a mere village?! Pathetic!"
I've never, ever seen this happen outside of video games, so maybe that's why it seems so foreign to me. The "go kill those three random skeletons and dire rats in the cellar" has never been something I've seen.
Let me give you a few examples from the few 1st level adventures I just looked through.
The Sunless Citadel's first encounter is with 3 dire rats who are just hanging around the dungeon's opening. Later there are dire rats hiding in refuse piles and cave rats, and more rats later on. As well as a hidden room that has skeletons just hanging around inside.
Pathfinder's "Crown of the Kobold King", the adventure is all good and heroic - but here we have dire rats just sitting in dungeon room minding their own business, the PCs barge in, the rats attack.
That's a good comparison 1st level pcs and 15th level PCs. You're right, 15th level PCs would kill rats and skeletons trying to hurt people. But, you wouldn't actually run the numbers. You wouldn't roll to-hit for a 15th level PC to kill rats and skeletons - you just assume they do because they're not a challenge and you don't want to waste time rolling it. Like saving a kitten from a tree, it's something a good person would do, but you wouldn't dwell on the success of it because hey it's a freaking kitten in a tree, we don't need to roll multiple climb checks, just handwave it and move along.However, even if it was, I know that the heroic characters at any level would help any way they could if they were dangerous. I'm assuming the party can fight dire rats or skeletons at low levels with the same intention that level 15 characters would: helping people. I think you're talking more about context than creatures, but I might be wrong (there's a big difference between dire rats randomly attacking from a pantry, and dire rats harassing town members by eating their food and diseasing them).
Set aside the "Hey they're attacking innocent people" angle (because I've rarely if ever seen that's the case with rats and skeletons), and just put them in a room in a dungeon. Now tell me how awesome it is to fight them. And yet rats and skeletons are a "challenge" to 1st level PCs. They are Legitimate threats and posed as such to kids poking through a crypt. I just find that insulting. I use rats and skeletons as a bit of a hyperbolic example, but it invokes the feeling of fighting bugs because you're not good enough to face any real threat, go grind until you're a higher level.
In one of Paizo's Rise of the Runelords adventures (I think 5?) the PCs are about 14th level, and they are infiltrating a library where an army of giants are camped outside. Inside, they come across a room with some CR 5 ogres. The fight is played for laughs - the ogres try to push the PCs into mud because they think it's funny, and pose no real threat to the PCs because they simply can't touch them. It's not dangerous, it's just the PCs squishing some bugs that potentially could harm someone much, much lower level than them, but who aren't. That to me is killing rats and skeletons.