Simple scripting will do the job:

#!/usr/bin/env python
# Report uniquely aligned pairs from BWA sam output.
import sys
i = 0
uPair = 0
lines = ''
for l in sys.stdin:
  #write header info
  if l.startswith('@'):
    sys.stdout.write( l )
    continue

  #reads
  lines += l
  i+=1
  if 'XT:A:U' in l:
    uPair += 1

  #every two reads  
  if not i % 2:
    #check if both are uniquely mapped
    if uPair == 2:
      sys.stdout.write( lines )        
    uPair = 0
    lines = ''

I would just use 'grep' to keep the headers and the line matching the tag:

/samtools view -h -f 0x002 file.bam |\
egrep "(^@|XT\:A\:U)"