The issue we are facing is that deletes also get auto-batched making the batch processing slow.

What's the recommended practice to handle deletes now since documents are no longer soft deleted.

There is none, the task queue will process the task index by index.
However, you could swap the indexing process more often by reducing the number of batchable task in a row by using the MEILI_EXPERIMENTAL_MAX_NUMBER_OF_BATCHED_TASKS env var (⚠️ it's an experimental feature)