As someone who plays Domination way more than any other gametype that seems fine for me. Unless it's a 100% perfectly symmetrical map one team is going to get screwed on getting to the middle territory (how unbalanced this has been has always varied from map to map in every game). I'm assuming that it's still the same 3 capture points, but that the teams basically swap their starting points for the second round. Seems fair to me.
I do get the complaints though in that maybe you've set up base really well at a particular territory or whatnot and will lose that if it's in the first round and it forces the round change. Personally I'm willing to break each game into two "mini" games (if you will) to have a completely level playing field. I suppose it's hard to say 100% for sure without playing it, but at least on paper I'm okay with it.