Hello (first post on forum, i'm intimidated ^^')
A basic solution to reduce the issue would be to automatically merge the isolated enemy ships into a fleet as large as enemy current logistics permits (i think endless space did that). It makes sense since if i was a pilot, surrounded by allies, seeing a big fleet coming in my way, i'll call my allies to join the fight instead of going alone to be slaughtered alone! 
This merge shouldn't include non combat ships as it also make sense that you join a fight only if you have weapons to fight! (should it work if there's only non combat ships? not sure... make sense for non combat ships to disperse if attacked)
However, this solution only reduce the problem since:
- it would only work on one hexagon (which means still have to make your way through a bunch of dispersed small vessels)
- it's limited to the logistics capabilities of the enemy, which can be quite low
A more advanced solution should be to include all hexes surrounding the attacked hex into the fleet merging => clean 7 hex in one go.
An even more advanced solution should be to get rid of the hard cap on logistics capability and replace it by negative things like friendly fire, defense reduction and so on (the more beyond the current cap you are, the more maluses).