I think you need to work out how likely she is to get her first choice. Do you meet any special entry criteria? Or will it be purely on distance? If so, how far do you live from the school and how far away did the furthest child admitted live last year (and preferably the year or two before as well).
If you are happy with the year 6 place then take it. You might or might not get into your 1st choice school. If you did get in to your 1st choice school then you can make a decision whether to stay. Don't forget when children go to secondary school a lot of times they get new friendships anyway. I moved dd in year 6 to a school that automatically moved them up to the secondary part of the school. I too wondered if it was the correct decision as dd had a lot of friends at her primary school. Dd was very upset to be leaving but from day 1 in her new school she has never looked back. She has made loads of friends and her only upset is that at sometime she has to leave.