This can be accomplished at the time of processing the transactions in batch.
  1. Process transaction into a batch
  2. Go to the column marked NetCommunity Gift 
  3. Unmark the checkbox
  4. Repeat steps 2 and 3 for any gifts in the batch that you would like to not be marked as NetCommunity gifts
  5. Commit the batch

When you review that gift transaction in the record, it is not marked as NetCommunity Gift in Raiser's Edge.