Leaving aside the issue of whether the passenger could have eaten the omelette after it was being tainted by the pork (ie cultural insensitivity on the part of the FA), I don't see any problem with her using her fingers to remove it.

If there was a shred of paper on the top of my omelette and the flight attendant noticed it while she was serving it to me, am I really supposed to expect her to get a fork (which if serving in J class is not readily available on the serving trolley) when her using her finger works just as well provided it makes no contact with the food I end up eating?

I'm not so pretentious so as to demand something be done when in fact it makes no impact on the hygienic standard of the meal. It's not like she's grabbing the omelette off a main serving dish and plopping it on the diner's plate with her hand.