Either method will work for reconfiguring interfaces. I typically don't like to source /etc/rc because you end up with duplicate commands which sometimes generate errors, but that is just my preference.
For flowcontrol settings, though, I think the interface may need to reset, which may be why NetApp wanted a takeover/giveback. The NMG says that the flow control setting is advertised during autonegotiation. If the link is already negotiated, I'm not sure changing this setting will have an effect. You could verify on the switch end, and if it doesn't take effect you can offline/online the switch port, which should force a negotiation - again, you've redundant links so this should be okay.