In general lack of stability in a family is going to be confusing or even damaging for children. That much ought to be uncontroversial.
But also what ought to be uncontroversial is that children have to learn about the world around them, and their formative years can be very influential. If you teach a child that children of different skin colour, or parents of the same gender, or even people with visual disabilities, are normal or at least not to be frowned looked down on, then the child will not look down on or be suspicious of them. On the other hand, if the issue isn't addressed at all but left until later -- this is the sort of thing that leads to discrimination, or lack of comfort when spending time with people who are different.
Moreover, for all that you get offended at the idea that children are projecting their parents' homophobic views -- well, that's the sort of thing that does happen. A few years ago there was a massive fuss about an amputee presenter on CBBC. What seemed to happen was that children would ask their parents, "Mummy, was hasn't that woman got a hand?" and a lot of parents didn't feel at all comfortable answering the question. Is the child afraid of the amputee? No, just curious. The child will be afraid if the adult acts like there is reason to be. Conversely, if the adult had answered calmly then where would be the problem?
Like it or not, same-sex marriages are here to stay. The absolute worst thing we can do now is to try and hide this from our children and hope that it will all turn out OK. Instead we should teach them to be tolerant, accepting, and to keep their noses out of other people's family life.