It is possible to turn the auto-attack option of your fleet to false. That way, they won't attack the enemies scouts. This helps in two ways: You can leave your fleet at the repair station(s), and you won't lose any hard-won reputation with that AI player if you destroy the scout.Also, research PSIDAR (or its non-TEC equivalent), to know when an enemy fleet is approaching your planets. That way, if its just a scout, you can always turn off auto attack. If its a large enemy fleet, just turn it back on.
Yes I ended up turing auto-attack off. But it is still my opinion that this is not an effective use of my time/attention:
1. Get alarm enemy fleet is approaching
2. Check fleet to see if it is a scout
3. Turn auto-attack on my fleet off so it ignores the scout
4. Wait for scout to leave
5. Turn auto-attack back on
As opposed to this:
1. Check "Ignore scouts" option at the start of the game.