I read Tom's situation like this. He's an alien and knows it. He replaced the orriginal Tom years back in the plane crash in the everglades. He was a scout or something for a later arriving force which finally came in the hurricane. During the time he was scouting and waiting he met, fell in love with, and married Muriel. Now the woman he loved has been killed and replaced!
This puts him in a difficult place emotionally. He really loved his wife and now she's gone. But as long as she thinks she's normal and acts normal, he can continue pretending that she's the same person. You saw how different her attitude was after she returned from finding her body. Those that KNOW they are not humans just act differently. Like the girl killing the mother in law and not wanting the baby. When you know you're not human it's kinda hard to pretend and act like one. Tom had to do so because he was the only one around. Now that the invasion seems to be kicking into high gear, the new batch doesn't feel the need for the same level of secrecy.
So I could definately see Tom eventually turning to the side of the Humans and helping them. Especially if the invasion doesn't end up being what he was told it would be. Wouldn't be the first time superiors lied to a grunt in order to get him to do the mission.
As for why he lied to Muriel about seeing the body, again I think it's to make her question the replacement thing. He'd rather have a confused version of his old wife think she's insane than an alien he doesn't love running around in her body!
