I wouldn't worry about September at the moment. Keep the place at the secondary school, obviously, but cross that bridge when you come to it.
I originally took my younger daughter out in Year 4 just as a reaction to a situation she was in in Year 4. I fully intended to send her back in Year 5. However, I thought I'd worry about that when it came to.
In the end, she never did go back because HE worked so well for us. But we did look at secondary schools for next year (she's Y6 now too), to give her the option. In the end she decided to keep going as she is. Big sis (Year 9) is now also HE and it's not nearly as hard as I thought it would be!
However, if you'd asked me to even contemplate educating them through the secondary years when I took DD2 out in Year 4, there's no way I could have done it!
Secondary will be a whole new beginning, so I don't see the arguments that she will necessarily not want to go. If you both decide at the time to continue HE, fair enough, but HE children I know have returned to school for various reasons with no problem. I don't see that the taking her out for a short while is any issue at all. In any case, I think her needs at the moment sound more important than worrying about September. Sometimes you just have to take life as it comes.
I can't promise she will definitely want to return in Sept, but you do have on your side that if it's really not possible for you to continue after then, you can talk through with her why and she is old enough to understand. What I would do is put school to the back of your minds for a short while, to give her a chance to really make the best of the HE. We did this a lot at the beginning. I took DD2 out in the October half term and we were all a bit wobbly over it, so we said, we won't talk about returning to school at all until Christmas. Then we discussed it at Christmas, decided HE was going great, and said we would review it at Easter. We don't need to do this any more but it was a useful exercise at the time because it enabled us to put the topic of school out of our minds, whilst still knowing we would return to discussing it as a possiblity. I'd say the June would be a good time to say you will forget about all school until. Secondaries usually start their induction days around late June, early, July, so then would be the time to start discussing school again.
I wouldn't worry about HE not being a "positive choice" at this stage. We took our girls out because of a negative reaction to school and it was the best thing we ever did. Sometimes things you do to resolve a crisis situation end up being things you wonder why you didn't do all along!
If she wants to come out of school, I think your decision is made. I think you have nothing to lose and everything to gain.