Using the output command as per your example, create a file sql.sql containing something like:
select 1
go
output to 'c:\temp\output.txt' FORMAT ASCII
DELIMITED BY ',' QUOTE '''' ALL ENCODING cp1253
Then run:
# ./dbisql -host <host> -port <port> -c "UID=<user>;PWD=<pwd>" -c "UID=<uid>;PWD=<pwd>" -nogui sql.sql;cat /cygdrive/c/temp/output.txt
'1'