How to avoid apps being re-arranged when synching with iTunes?
You could disable App syncing completely on the apps tab. Then iTunes will not sync the apps anymore and so it won't re-arrange them.
The drawback is that new apps won't be downloaded to your Mac/PC anymore. So in case you have to restore your iPhone using iTunes you will have to re-download all the apps. But as your purchases are connected to your Apple ID you will not loose the apps. They're just not stored on your Mac/PC.