Does John Locke (Second Treatise of Government) regard women as equally free by nature or as naturally subordinate to men?

Be aware that Enlightenment thinkers tended to view women as collectively inferior to men in terms of temperament and capability (as did Europeans during the Enlightenment in general). The inequality between the sexes is a common theme within the Enlightenment, and it was defended and reified in the Enlightenment's appeal to reason, through which writers and philosophers could construct arguments and schemas of classification, further supporting the sexism which underlined Early Modern society. With this in mind, we should not be surprised to find Locke mirroring those same underlying sexist assumptions which the vast majority of Enlightenment thinkers tended to support.
Part of what's tricky about your question is that Locke himself doesn't talk all that much about women in the Second Treatise (though that silence in itself is very telling). That being said, you should consider that this entire treatise was centered upon the question of how "civil society" has come into being, and in the Early Modern Context, civil society was dominated by men. If Locke were to have supported the natural equality of the sexes, it would have raised critical questions and criticisms about the inequalities present in his own society, but he is notably silent on that account. Furthermore, consider that Locke's writing is itself dominated by gendered language.
Finally, I want to note that, while he does not speak much about women in particular, there are several places were he does make comments that adhere closely with Enlightenment assumptions as to the natural inequalities of the two sexes. In his First Treatise, for example, he states the following:

God, in this text, gives not . . . any authority to Adam over Eve, or to men over their wives, but only foretells what should be the woman's lot, how by his providence he would order it so, that she should be subject to her husband, as we see that generally the laws of mankind and customs of nations have ordered it so; and there is, I grant, a foundation in nature for it. (chapter 5)

Later, he reiterates this same theme in the Second Treatise, in its seventh chapter. Here he discusses what he considers the "first society"—that being between husband and wife. However, this should be understood as something separate from and ultimately transcending large-scale civil society because this particular relationship had the effect of ensuring the continued survival of the human species. This is, for Locke, the first and most fundamental of relationships, and he views it as unequal:

But the husband and wife, though they have but one common concern, yet having different understandings, will unavoidably sometimes have different wills too; it therefore being necessary that the last determination, i. e. the rule, should be placed somewhere; it naturally falls to the man's share, as the abler and the stronger." (chapter 7)

To conclude, it does seem that Locke holds many of the same assumptions which were common in the Early Modern Era as to the inherent inequalities between men and women.