Well - After several games with 2.5 beta, and reading alot of posts on mines and mine sweeping - I have an idea.
Do you think that if the scout had a reduced mine detector range and a special pulse (with one very long cooldown period) that could temporarily disable the visible mines for a duration that suits the game balance.
This would have the following effects.
1. The possible need for several scouts to disable a section of minefield to allow your fleet through.
2. Disabled mines could be destroyed without doing any damage by your ships.
3. Your fleet would need to push past the minefield quickly and perhaps pushed into the enemy players defences, ie starbases.
4. If the battle goes badly retreat could be a real danger as the mines have reactivated - maybe you would have to do option 1 again!
5. Makes mines useful again - the defending player would know what was going on, but if the opposing player sends enough scouts to disable the mine field its possible that a big enough hole is made to bring a fleet through.
6. The scout pulse could be set to right click auto-cast (complete with waypoints) to reduce micro-management.
Edit - Its been said before, but I think mines that are triggerd by an enemy should damage everything - your own ships, the enemy - structures, the lot.