At least two churches have decided to abstain from referring to God exclusively as "he".
The United Church of Christ.
The Eleventh General Synod instructed that a Book of Worship be developed and characterized by language that is truly inclusive with respect to God and to people. Although the generic use of masculine terms has been accepted practice, it is exclusive and viewed as offensive by many. Further, the use of only masculine nouns and pronouns for God and of masculine generic terms for humankind has hidden the rich feminine imagery for God and God's people in scripture. Scripture contains many gender neutral metaphors for God such as shepherd, rock, or Holy One. The rediscovery of the complementary female and male metaphors in the Bible and the literature of the early church encourages Christians not to settle for literary poverty in the midst of literary riches.
And the Metropolitan Community Church.
Many of us, when we first come to MCC, are so accustomed to using male pronouns for God that even when we come to understand God as beyond gender and other human categories, even when we come to view God as Spirit who is neither male nor female, it is still difficult not to say "he," "him," and "his" for God. This male terminology, however, limits God to our cultural view of the Divine, which is a male-dominant point of view.
~Reverend Dr. Jeffrey Pulling, "More Than Just Words: A Study & Reflection Guide to the Issues of Inclusive Language Within MCC"