You won't get a check engine light from removing the resonator pipe. The resonator pipe is just used to change the exhaust noise to a nicer sound.

From King Midas:

WHAT IS A RESONATOR?
The resonator is a second , usually smaller silencing element in some exhaust systems where the space available under the car does not permit installation of a muffler that can completely silence the exhaust. The resonator smoothes out any loudness or roughness from the first muffler. Most resonators are located to the rear of the muffler.