Tente isto:
SELECT port
FROM interfaces
ORDER BY SUBSTRING_INDEX(port, '/', 1), CAST(SUBSTRING_INDEX(port, '/', -1) AS SIGNED)
Verifique a SQL FIDDLE DEMO
SAÍDA
| PORT |
|--------|
| Fa0/1 |
| Fa0/2 |
| Fa0/3 |
| Fa0/4 |
| Fa0/5 |
| Fa0/6 |
| Fa0/7 |
| Fa0/8 |
| Fa0/9 |
| Fa0/10 |
| Fa0/11 |
| Fa0/12 |
| Gi0/1 |
| Gi0/2 |
| Null0 |
| Vlan1 |
