I think there is too much room for error even having a check box. People really don't always check everything - I know I don't. and to accidently have that box checked could be disastrous. Only workaround I can think of is to write a script that goes through your folder of limages and looks for files that have the _1 appendage then have the script delete the original and rename the new file.
As a potential work around, if Photoshop can identify the “event” of opening a file from ACR rather than as a standard “open” command, then the Photoshop Script Events Manager could possibly automate the saving/closing of the ACR “edited” JPEG. Otherwise as Chuck states, this pretty much defies the mantra of ACR/LR of “non destructive editing”.
Thanks for the responses.
I guess the answer is to create a sub folder and put all the camera jpegs in it. Then use ACR as normal. Then copy all the original jpegs back chosing to skip any which would duplicate. Then delete the folder. A bit of a pain, but quicker than opening/saving all the new jpegs.