Right now a fleet with "Pursue: On" will destroy a number of structures that I don't think should be destroyed except by deliberate request of the player. These are basically "AI Progress reducers and things you will want to hack." It's very frustrating being unable to easily destroy the defenses of a planet with a DesignTemplateServer without trusting your own units to not kill the thing you want to hack....
Here are the structures:
DesignTemplateServer
SuperTerminal
DataCenter
Coprocessor
EMP/Lightning/Nuclear warhead silo
I think these structures should have the following XML field set: player_units_do_not_attack_unless_taking_planet="true"