Tom is most definitely not innocent. I don't know how just yet, but he is definitely not innocent.
Also, the people interviewing Tom and Gina (or whatever that last woman's name was) have got to be the most incompetent government employees ever. Liz asks her if she's ever seen the man whose picture was found next to her bed, she says nope, and they're all like, "Well that's good enough for me!" Then after interviewing Tom they drag him out through the area where they have all their classified information hanging on walls. You'd think they would have him use some nondescript hallways with no confidential information, but no they walk him right up through the nerve center of their operation. Solid job guys.