But from the viewpoint of the Ordinals/soon Runes users, if they have paid the fees and they're transactions are following the consensus rules, are they truly "exploiting" the system?
Yes. In the same way, you could try to copy-paste the whole chain from some altcoin into Bitcoin, by using "a coin in a coin" scheme. Or copy-paste all posts from bitcointalk and put it into Bitcoin transactions. Or even abandon GitHub, and copy-paste all commits behind "OP_SHA1 <commitHash> OP_EQUALVERIFY <developerPublicKey> OP_CHECKSIG". The purpose of Bitcoin is not to be "the global chain for every use case". As Satoshi said:
Piling every proof-of-work quorum system in the world into one dataset doesn't scale.
And then he also continues:
Bitcoin and BitDNS can be used separately. Users shouldn't have to download all of both to use one or the other. BitDNS users may not want to download everything the next several unrelated networks decide to pile in either.
So, if other use cases would use some separate chains for that data, it could be fine. They could build some honest, valuable protocol out of that. But the problem is, that they just decided not to, and abuse the Bitcoin network instead.
And yet another sentence, from the same post:
The networks need to have separate fates. BitDNS users might be completely liberal about adding any large data features since relatively few domain registrars are needed, while Bitcoin users might get increasingly tyrannical about limiting the size of the chain so it's easy for lots of users and small devices.
Which means, that if you put all of those additional features on separate chains, then Bitcoin can still stay "easy for lots of users and small devices", and just take a role of "a notarization chain", providing Proof of Work to timestamp all other chains. But if you put "everything on Bitcoin" instead, then guess what: the current limits will take down existing payments. Because it is always a choice: confirm this payment, or this Ordinal. Which means, that if you allow using and abusing Bitcoin for everything else than the payment system, then it may stop being useful for payments, and lose its utility.