Personally I've never found COL's to be that much of use since they're so ...clumsy... Also they're cruisers, so one could take three de's for the same CP cost.
However, if you bring several Wild Weasels with your Dronefleets, those interceptor missiles are happy to home in on those. Phasers are drone-killers tho.
If you still want to use drones against phaser pd's, then you should invest in torpedoes and mirv missiles. MIRV's simply because they can take a bit more punishment than other missiles (except perhaps nanite missiles, but those are a bit hazarduous with drones
Laser PD isn't really a much of a problem against massed drone fleets (perhaps with the expection of the Liir... damn pd-maniacs). If your enemy goes for lots of Gauss PD, just add plenty of missiles to the drone fleet and you're golden again.
Orbital foundries... I don't really see what the problem is, for some races destroyers are far better than cruisers until mid-late fusion. For some cruisers are essential anyway.