I'd say definitely tell your sister that she's out of line. No drama, just tell her that you already know her opinion on this and you strongly disagree and don't want to hear about it anymore. Set boundaries for yourself and stand by your partner. Extra points if you add a couple inches of heel just to make a point ;).

Also, as a 5'5'' dude I gotta tell you: these short man/tall woman/heels blah blah blah stories do get old sometimes, but we're socially banned from voicing our opinions (because it's "evidence" that - ha, knew it! - we are constantly self-conscious about our height). So it's always nice when someone gives the shorty-haters some stick on our behalf.