Well if you know how to tell if a deal is faulty through visual inspection, then you need to program/build that logic if possible. Sorry can't tell you how to check for faulty deals without know how you did it manually.
CRM_ORDER_READ is pretty database intensive especially if you are handling that much data. My only thoughts if you aren't doing already, make sure you are only requesting the segments you need to perform the check instead of reading everything. However I bet you already doing this. If I were an SAP salesperson(which I'm not), I would tell you just put HANA underneath your SAP CRM system and your performance problems will be solved 
. However you probably don't have the budget nor the time to wait for that to happen and meet the deadline for your requirement 
.
Take care,
Stephen