Hi niraj,
Yes, we have observed the mapReduce performance issue in both TokuMX as well as PSMDB using the PerconaFT engine. Your observations regarding the delete messages are also correct. Node deletes are the Achilles Heel of the fractal tree. Sadly, now that PerconaFT has been deprecated for PSMDB and Aggregation Pipeline is now preferred over mapReduce in most scenarios, it is not on our road map to address this issue at the present time.
If you require mapReduce functionality, I recommend migrating to Percona Server for MongoDB with the rocksdb or wiredTiger storage engines.
–Dave