Did you forget about heavy fighter/bomber attacks? Despite flak and AAA, capital ships are still very vulnerable to fightercraft, and given that intersystem drives for fighters are still extremely expensive at the time of FS2, the fightercraft you need to counter the enemy's need to get to the right system somehow. Enter the destroyer.
I didn't, but I don't know how expensive "extremely" is. I might still rather risk several intersystem drives than a destroyer. If the destroyer jumps in, then it probably won't get to jump again. Even if it does, it definitely won't get to jump a third time before getting attacked by bombers from the enemy destroyer. It could launch more fighters, but on the other hand it would be a giant target. So the destroyer could only enter the system at the end of the offensive, fire everything, and secure the node.
But, uh, that's all speculation right now. 
Destroyers provide more than just a fighter launch pad. they are also:
mobile repair and resupply centres for fighters,
provide tactical mission support with the resupply ships,
having a destroyer in system shortens turn around time for fighters by making jumps shorter and removing the lengthy inter system jump stage between missions,
in system command and control for friendly activities means faster command response to changing situations.
large area target location and tracking, even in hostile territory.
In FS fighters and bombers are best used as force multipliers rather than the backbone of your efforts, they are short term force projection. If you want to hold territory you need a capship and we know how vulnerable they are without fighter support.