I think the best thing the church can do is stop devaluing femininity, stop treating womanhood as inherently weak or lesser than manhood, and stop pushing such a narrow, stereotyped, superficial definition of femininity to begin with.  

Of course most women will reject femininity if they are constantly sent the message that it is all about being pretty, quiet, helpless, passive, and boring.  I think a lot of women are naturally feminine, but they also posses qualities of strength, ambition, intelligence, and drive.  It's not so much that they aren't being "womanly", but that we don't allow our definition of womanhood to have any interesting, active, or dynamic characteristics.

In short: women will be more comfortable being women once Christians (and secular society, too) get over the idea that girly stuff is stupid and lame.

We also need to stop shaming women who naturally embody tougher characteristics.  So what if she's a tomboy and looks like one?  Biological sex isn't the main thing that determines one's personality (your reproductive organs are not the same thing as your gender qualities).  Also, women don't exist to be your ornaments or to make you feel comfortable by fitting in a non-threatening little box.