Hmm...if I had to guess I'd say it's the updating of the search index that's causing the timeout because that's done before any actual deletions. But I don't know of a way around it. I suppose it might be possible to delete your search index, delete the threads, then rebuild it (although rebuilding it might then time out). Do you have any way to increase the timeout? (Maybe talk to you host and tell them you just need it temporarily).
Hopefully someone else will have a suggestion.
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