Besides the light issues, it looks like they were sowed too shallow, and the seedlings have just a whisker of the root in the ground. You can easily lose them in this condition (I know cause I've done it and even keep on doing it with some kinds of seeds!). So I would not wait for them to get another leaf before getting them deeper in the ground.
Simplest would be to poke a row of holes with your finger, in the space between the present rows, then take those up one by one, pop it down into the hole, and close. Again, i do this all the time and tomato seedlings will be fine with it - just make sure nothing is too dry before you start.
You could, alternatively, top up the container with some more potting soil to cover the long bits, but you would have the dickens of a time trying to separate the tomatoes later.
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