Unfortunately, due to limitations in the backend, there is not a way to close the app via RPC. I'm not sure if Windows provides a 'kind' way to request an app exit or not, but yes, if you kill BitShares, it will assume it crashed and offer to nuke the database for you when it starts up again. This is strictly optional, you do not have to do it; just click the "Continue Normally" button and it won't rebuild the database unless it detects corruption in it.
I will look into adding a way to request the client exit by using a new instance as a remote control to a previously running instance. This should give you a nice way to quit BitShares X from your batch file.