My 2c:
hastop -local was executed before bringing down applications manually which resulted in appsg to go in faulted state.
Seems something is wrong with Service Group config.
hastop -local will offline all online service groups on the local node. This should not leave your appsg in faulted state. You need to double-check your config and see what errors were reported in engine_A.log.
I am going to move rc2.d and rc3.d scripts for VCS on both the nodes
Where are you moving these scripts to?
Seems you want to do a permanent move and not just temporarily for System Maintenance?
Best Practise for System Maintenance is to bring system up to single-user mode (rc1/rcS).
Offlining SG's before freezing is best practise.
arangari has given best possible solution.