I think even if you are tolerant and accepting of that sort of stuff, it's easy to find yourself in a bit of an awkward position when you're sat as Laporte flirting with your same-sex superior officer. It's not something I'd find awkward in the slightest if I was sat on the train reading this in a book, but to actually play as the character and have that sense of 'involvement', I guess you could call it, has the potential to leave you sitting there feeling something between 'Well, this is new, interesting, and totally fits in with who I saw Laporte as in this new-age society' and 'Um, this is a little weird. You're my Squadron OC and the Frigate CAG, and my character is flirting with you. mmkay.'
Either way, it's something I envisage you get more accustomed to with exposure. I didn't find it so detrimental to the story, but during testing I felt like it hit me from left field the first time I played.