Why would you need to straighten the marching ant selection? In doing so, you would only straighten the selection and not the layer (map) that was duplicated with the selection if you're using the selections properly.
If you use free transform to rotate a selection before it is pasted to it's own layer, then you will cut holes out of your map. This will then affect any overlapping needed for the next map section.
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Or you can go to SELECT > TRANSFORM SELECTION to alter a selection without affecting the map layer, but you're only moving the selection and not the map section.
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However, if your asking about an automated way to straighten the layers of map sections created by the marching ant selections, then there's none that I'm aware of at the moment. Once all the map sections have been made, you could possibly place them in a folder and create an action or script to straighten them. This is outside my wheelhouse.
You want to straighten the map sections after they have been pasted to their own layers.
This is not what I have experienced. It works perfectly for me.
Here's proof. I set up guidelines to test the accuracy of the straighten feature of the Ruler Tool. Works perfectly every time.
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I'm not saying that this is the only way for you to do this, it's just the easiest and fastest way I can think of for the moment. With only 50 map sections to make, this would only take about 15 to 20 minutes to complete, maybe less. In the time that you have spent trying to find a way to automate the process you could have been done.
