DS1 wasn't coping with primary so we took him out in Y6, gave him time to chill out and relax and then hoped he would go into Y7 ok - which he did. Everyone at the time said that HE would just make him worse - he'd get used to being at home and then would find it even harder to go back to full-time school. I also worried about this myself and was far from convinced that it would work but we got so desperate that we just had to try. It worked out brilliant and the break gave him time to relax and he started secondary with no problems.
However, do you think this is unusual? We are now in the same boat with DS2 and I'm doubting myself again - maybe the luck we had with DS1 was just that... luck. Is it more likely that he'll find secodnary even harder after being HE'd?
(I'm perfectly happy to HE at primary level but not happy to do it at secondary).