It was clearly Gene Roddenberry's intention to challenge social prejudices. The original series would have been cancelled but for a fan petition, and it went on to become a franchise that has made you good money for over 40 years. Star Trek has examined race, gender equality, politics, religion. Sexual orientation is conspicuous in its absence and it's hurting the brand. Trust the fans again on this, and your franchise will be profitable for another 40 years.
My other comment would have been that if a tv production team from over 40 years ago was creative and clever enough to hide a close relationship between Spock and Kirk out in the open, then surely a badass modern film creative team can push the envelope the same way and remain acceptable to the majority of their audience.