I know most of us probably think Milton did it, but I think there is a very possible chance that Martinez could've done it. People have been pointing out that Martinez's comic counterpart is a bit more sly, and his TV counterpart is more "straightforward."
IMO, Martinez's point of view towards the prison survivors changed after he met Daryl and has a slight talk with him. When they arrived back at Woodbury and the Governor orders him to prepare men out to kill everyone in sight when they meet next, Martinez acknowledges it, but doesn't show that "slick smile" that he usually does whenever he kills something with satisfaction.
I have a theory that Martinez may start to feel that this is all going out of control, but do not trust anyone to share his point of views with. He watches closely when Tyress and Allen fights over it's ethical to unleash the biters, and may have "secretly" concluded on who he can recruit / trust if he is to go against or attempt to escape Woodbury.
The Governor may have a slight distrust over Martinez as well now, since he also lied to him about not finding Andrea. In the end, I believe it would be Milton and Martinez rescuing Andrea, and bringing Tyress, Sasha, and maybe some random people in an attempt to join the Prison.
Of course this is all just my opinion.