Should the BIP 39 mnemonic sentence checksum be eliminated from the standard? Does it do more harm than good? Should the BIP 39 checksum be eliminated from the standard? Should the BIP39 checksum be made optional to improve security?
No, I don't think the checksum should be removed or made optional. It doesn't do more harm that good.
Bip39 is a simple way to copy computer-generated randomness from the computer onto, eg a piece of paper. This Bip39 mnemonic sentence can then be used to restore your wallet, should you lose your computer. The checksum provides some degree of certainty on the correctness of the mnemonic you enter.
However, lately, people have begun to explore how to create their own randomness when creating a new wallet. This can be done with dice, coin-flips, etc. You might want to do this for example if you don't trust that the computer's random-number generator is doing its job well.
Since most wallets offer a way to restore a wallet using bip39 mnemonic sentences, people are trying to use that feature as a way to create new wallets from manually generated randomness. This is where the problem lies.
Actually, it's stated in the Motivation section of bip39:

This guide is meant to be a way to transport computer-generated randomness with a human-readable transcription. It's not a way to process user-created sentences (also known as brainwallets) into a wallet seed.

So we're actually using bip39 in a non-intended way, and that's why it's so awkward. The solution to this is not to modify bip39, but to acknowledge that we're doing it wrong.
Instead of entering manual randomness into a computer through bip39, we should invent other means of transferring the manual randomness into the computer. Some wallets already offer this. For example, ColdCard lets you input dice rolls one by one until you think you have enough randomness and then the device will provide you with a bip39 mnemonic sentence for you to backup on paper. That's one way to do it.
As you may have noticed, since writing about this on Twitter (cited in Michael Folksons's answer), Mastodon, and Reddit, I've changed my mind about this. I no longer think that making bip39 checksum optional is the solution. The solution is to not use bip39 to input randomness into a computer. The purpose of BIP39 is to transfer computer-generated randomness to a human, not the other way around.