This should work better:
echo fr=domain reply=1 command=scrap_wafer comment="Success" | sed 's/.*reply=\([[:alnum:]]*\) .*/\1/'
the problem was that the dot inside the \(.*\) expression matches any character including a blank space, so that if you have more field after reply=something, separated by spaces, all of them (but the last one) are matched. The expression [:alnum:] matches alphanumeric character only, that is spaces, tabs and punctuations are excluded.