Wrap it in a keyboard interrupt exception and replace os.system with subprocess.call.
Please not that for convenience of path resolution, I put the shell=True argument in, but that has security implications you should invalidate before doing this.
import subprocess
try:
subprocess.call("python run_me1.py -lines -s {0} -u {1}".format(args.start, args.until), shell=True)
subprocess.call("python run_me2.py -derivs -tt", shell=True)
if args.mike: subprocess.call("python run_me3.py -f derivs.csv tt.csv", shell=True)
subprocess.call("gnumeric derivs.csv", shell=True)
subprocess.call("gnumeric tt.csv", shell=True)
except KeyboardInterrupt:
print("exiting early")