How to avoid calling FieldCollectionItemEntity::deleteRevision
Copy and Paste your own version of the FieldCollectionItemEntity class file and call it like FieldCollectionItemEntity2. Then simply like have FieldCollectionItemEntity::deleteRevision return or do a NO-OP. Use the new class in your migration instead of the default one you're using now.

For when the migration completes; implement like a PostImport() function to delete all but the most recent revision.

To my knowledge there is no Queue of revision items. A node/entity Save (and revisioning) I thought is done in a sql transaction statement.