Dear Sai,
The report SMO6_REORG2 calls many different reports and you can see the options for reorg different objects. You can define variants to separate the options in different jobs.
For example, define a variant containing only this one option "reorganize processed Bdoc messages" and schedule background job with this variant.
If this is still slow and the previous points are also considered, maybe the data is indeed huge. After running for the first time, you need to schedule this job regularly. Then next time will be faster.
Best regards,
Ellen