There have been a few posts in the past about detecting the presence of a current, or whether something is running. Try a search for the details - including the old forums, but the general idea is to use your CT feeding into a rectifier and smoothing circuit, and put that into a digital input (emonTH V1.5: D3 is the obvious choice), so saving on processing power (i.e. you don’t need to run for a long time, 40 ms or so to be confident you’ve detected a cycle peak, you can poll the input and go to sleep again immediately).
Or you could wire a neon across the pump and look for that with an LDR and a digital input with the right choice of series resistor (but remember neons flicker, and that’ll only tell you the pump has volts, not that it’s drawing current).
The circuit diagram (via the Wiki) will tell you which pins are available on your emonTH.
Secondary coil? I think you’re getting a bit mixed up here 
[Edit] A Thread or three: Current Sensor Utility line | Archived Forum
Problem with current sensor, or me! - #4 by Robert.Wall
Building a Yes/No current detector - #3 by Robert.Wall