I still think the rule needs to be changed. You should only be considered 'fleeing' if you dock with a base, use a jump hole/jump gate, or get more than 5000m from the enemy.
The only reason this zero-tolerance cruising rule was made in the first place is because people were using it to shield run or dock for repairs/ammunition, yet it completely cut out using cruise engines as a valid tactic in combat. They take several seconds to charge, they leave your weapons un-usable, there are already enough disadvantages applied by engaging/using cruise mode to make it limited in combat.