The scientists don't actually understand how the Spark works, they only know what it does. Note that it doesn't take any real skill to use it; in fact, when Sam is running away with it, he creates a number of feral Transformers by accident when he drops the Spark and it's energy just shoots out.
All Sector Seven was able to figure out was that running power conduits from the Spark into the chamber let them siphon off whatever energy it had, and they could fill the chamber with that energy on demand. Whatever that energy did to make a Transformer was still beyond their control, so all they could do at that point was fry the thing. The feral phone wasn't just turned off, it was completely destroyed with a high-energy bust that destroyed the electronics.
To try to scale that device up to the size of a full Decepticon would be very difficult, not to mention needing to get a Decepticon into the chamber to zap it in the first place.