I've been wondering about solutions to this problem. I came across this: https://github.com/BlockstreamResearch/cross-input-aggregation. I'm not sure, but maybe it could be a way to 'rescue' small utxos by combining into a larger value one.

Or perhaps some kind of shared channel batching with many inputs among different users, similar to a coinjoin. Batching reduces per utxo fees.

Perhaps these could be combined with lightning network hosted channels, which don't require an on chain transaction.

I'm not sure if there are any currently implemented solutions though. It could become a much more frequent problem in the future.