That's exactly what I do.
See my postbuild steps:
1. build out file
2. convert out to hex and add application CRC
3. flash hex via commandline tool
4. start debug (flashes out file)
=> application can read the CRC even in debug mode
problems:
1. double flash access => waste of time on debugging; not the best way for flash usage
2. command line tool uses other firmware for MSP-FET430IF as CCSv5.5
=> leads to firmware update on commandline access and second firmware update on debug start