After a bit of struggle I was able to find answer to my question. Since SCons is a python module by itself, it is possible to debug it in eclipse using PyDev. This is not the most optimal solution I wanted but was the closest.
Step 1: I disabled the Eclipse SCons nature of the project.
Step 2: Created a main file that will do the same function of SCons but instantiate the python object of the SCons main function.
Step 3: Set the breakpoints in my script where wanted and it was able to execute it.
import os
import sys
if __name__ == '__main__':
sys.path.append('/gpfs02/gcdistro/app/scons/2.3.0/engine/')
sys.path.append('/gpfs02/gcdistro/app/scons/2.3.0/bin/')
sys.path.append('/gpfs02/gcdistro/app/scons/2.3.0/engine/SCons/')
import SCons
from SCons import Script
Script.main()