If the doctor says she is okay, you might want to get a second opinion, but if he says she's okay physically for intercourse than it might be leaning psychological first... thus creating physical problems second.
How is her arousal? Sometimes, when a woman is not mentally turned on... even tons of lube won't make things pleasurable or get her mind of what she is fearing will be pain.
Does she masturbate? Has she ever had an orgasm? During arousal a woman can accomadate more that she could otherwise... if she is not having that build up of being turned on she might not be getting that swell on the insides that cushions the blows. Also when turned on you have more of a craving for penetration than if you are totally cold.
So lube is good... really good... but I would definitly suggest working on her sexual mood and relaxation as that will be what helps the lube to do its job.
If she can fit 4 fingers... (I can only fit 2... but I can accomadate my bf's rather large penis just fine when I am very aroused) she should be able to physically withstand your penis.
Do you manually stimulate her? Orally? Perhaps you guys can push the focus off penetration for a bit.. and just enjoy each others bodies other ways and let her gain some confidence and explore what feels good to her. Buy some toys smaller than yourself and work your way up to your penis as she gets more and more comfortable.
For me, after losing my virginity... penetrative sex did nothing for me (though masturbation did) for YEARS. I had sexual feelings but just did not appreciate the pleasure a penis could provide for a long long time. Since she is new to sex, perhaps she just needs time to develop the urge and to rid herself of anxieties about it.