Honda Civic 2000, Engine Control Unit replacement

As it is clear that the old ecu is damaged then if it does not start with the new ecu, then it definitely needs programming.

If it does start, then it may need programming for best performance etc

Unless its actually a 1999 then it should be equipped with a immobilizer. 2000+ Honda Civics all use transponders so if its actually a 2000 and one is starting with an all metal key then 1 of 2 things have happened.

1. The ecu was modified and the immobilizer was tuned out or emulated inside the ecu.
2. Someone has taped a key or transponder under the dash inside the antenna.

A proper ecu replacement will need to have the immobilizer tuned out again or either the ecu will need matching with the immobilizer system AND key with properly coded transponder inside. I usually prefer HDS (honda diagnostics software) or Autel's 908 but many tools can do these older Honda immo systems.