The real problem is that you're using the same table for OLTP and Batch processing. Load the data into a separate table (staging table), process it, the transfer the final results to your OLTP table.

We had the same problem where I work... code ran for 30 minutes, 4 times a day, and cause 10 minute long server wide "blackouts" each time. Using the method I've identified above, the code ran in 3.91 seconds...