Disabling build automatically option does not break JRebel. JRebel depends on the results of the compilation, so if you disable the automatic build you will have to just compile the changed classes yourself, that's it.
You can try setting a VM argument -Drebel.check_class_hash=true which will check the checksum before reloading the classes. It may slow down the reloading time from a few milliseconds to some milliseconds extra. But it is still better than the situation when all the project classes have to be reloaded.