It probably would be more efficient to remove OTUs prior to chimera checking, but I'm not sure the best way to do this with swarm.
Take a look at the pipeline described by Frédéric Mahé, in which he described this process.
Notice, he does chimera checking before OTU picking. At this step, you could also remove low abundance sequences. Then you take these reads and pass them into OTU picking with Swarm.
I know that does not directly answer your question, but I hope the notes of the swarm developer helps. He would be a great point of contact here too.