I would have thought that if it was illegal to have my DD 'known as' my surname, as opposed to the surname she was given when she was registerd, her school would have refused to allow me to have her listed on their register 'known as' my surname. The information I obtained when trying to find out how to go about changing my DD's surname to mine, was that if I wanted to do so, she would have to be 'known as' the surname I wished to change it to, for 2 years, before I could obtain a new birth certificate with the new surname. Then I'd be able to obtain a passport for her, with my surname. I can't change the original, as it's a historical record, but she can have her name 'legally' amended on a new birth certificate after she has been 'known as' mine for a period of 2 years. It might well be illegal to change or obtain an amended birth certificate without the permission of all those with PR, but I don't see how it is illegal to simply have the name noted on a school register as 'x' surname as opposed to'y'. I had no problems changing her surname with her doctor, dentist, library card - you name it, there was no issue whatsoever.
I spoke to my DD's nursery about it, and the head of the school she was to attend 8 months before she started, and neither of them mentioned anything about it being illegal. They were both very accomodating, and talked me through the best way to do it to make it easier for DD to understand.
I spoke to my ex, out of courtesy, and he had no objections to me doing this. If he had objected, I would still have done it. Technically, he doesn't have PR, but he could get it easily enough if this was such a big issue for him. The school and nursery are under the impression that he does have PR, and treat him accordingly. They have never seen her BC, so wouldn't know one way or another who is named as her father - only that I put his details down when she was 1st registerd. I didn't have her b/c to hand when she was reigistered, and they've never asked to see it since.
OP, I think you should speak to the school your DS will be attending, to get advice on this, and see how the school/nursery view this sort of thing and how they would like you/them to handle it. If they understand your reasons for doing this, and you handle this sensitively with your DS, then I don't think there will be any great problem with this. If you simply swap the surname's around, leaving your ex's as a middle name, then at least you are maintaining that part of the name for your DS. The way you have registered your DS is very similar to what we did when DD was registered, but I've now simply swapped the names around, so DD is 'known as' my surname.
If the school/nursery say yes, they'll amend the register, and any objections your ex has, or fuss he creates, won't automatically mean they'll change the name back just because he creates a fuss. It's far too unsettling to have the surname 'chopped and changed' IMO and I doubt they would be party to creating a situation that would unsettle your DS, with all the questions that would follow. I also think they would be more sensitive to how this looks to your DS, and if he has already been told, in a way he understands, that he is 'known as' your surname, they'll not just change it to keep your ex happy. Neither your ex's feelings, nor yours, are important - it's your DS's feelings that matter.
If you are worried about the fall out with your ex, get advice on how to go about it from the school, ask them questions about any problems you anticipate and see how they would deal with it. And if you can, speak to your ex about it - emphasise that you aren't changing the b/c, or his surname legally, he'll simply be 'known as' your surname with his still there as an unused part of the surname/middle name. If he still objects, then you need to explain the situation to the school, and see what they advise you can then be done i.e. leave it as it is, or change it to the 'known as' name. That might diffuse any 'fall out' you anticipate.
I've genuinely not been aware of this being illegal, in all the research I did before I did anything about it. This is the first I've heard anyone say it's illegal to to this. That is surprising to me, given that I've done it
and no one has said no, you can't do that, it's illegal etc.