Have been where you currently are with a hard to load horse. Horses do seem to be more comfortable with more room, but as some of the posters said above make sure you don't compromise the integrity of the trailer doing it. If I were you I would do one of two things.
1.) Trade that little trailer in for a roomier one - even an open stock would make your horse feel better. I look back when I was hauling 40 years ago and I wonder how we ever convinced our horses to get in those things
2.) I will be point blank honest here - there are too many good horses out there to have to deal with this problem. You really don't know if this horse will ever haul comfortably.
I finally got my horse to load and haul after a very long year and a half, but to be perfectly honest I could never relax while hauling that horse. I guess you could say I knew too much about her and what could happen... I sold her. Now my first question to anyone that has a horse I might be looking at "Does it load and haul?"
Just my honest opinion. I do wish you the best of luck with whatever you choose to do. Because I couldn't get comfortable doesn't mean you can't.