I would remove the male, like you said. Rats are generally very good mothers and it's odd to see litter after litter eaten. The only other idea I had is that she is a bad apple.

If it is indeed stress from having a male around, then yes I would remove him.

How close together are you breeding them? Perhaps the first litter was the first time jitters, but the second was too close, and she did not have the reserves to raise a litter, so she destroyed them. Rats will do this if they believe they are incapable of raising the pups, and will eat the litter to regain nutrition.

Just the fact that they ate all of the pinks tells me that this is not aggressive behavior, since when mothers destroy the pinks, they will sever the spinal cord, and often leave the bodies or parts littered here and there (sometimes not, it's a gamble). If she just picks them up and starts to snack, then I would have to believe she is replenishing her body.

Let us know how things go.