Here's a silly idea. I much prefer just tweaking the timer as suggested, it has a simple elegance to it. Therefore, the following is only an idea, and a half-baked one at that. The idea below does have the advantage of using a different resource.
Instead of an Exo-Galactic Strikeforce, just crib an idea from hybrids, and mobilize all (or some point value's worth of) the Mark X guardians in the galaxy. Before seizing the botnet, only MK1 Guardians mobilize. After seizing the planet, but before rebuilding, Mark II guardians can mobilize. Upon completion of the Botnet, the MK3 Guardians will mobilize. After that the usual timer/build count will start up, freeing up MKIV Guardians.
Alternatively, one planet's worth of guardian's piggyback on waves, one galaxy's worth of guardians piggyback on CPAs.