Sorry if this sounds harsh, but I don't see anything wrong with the reply (apart from the careless mis-spelling, obviously).
I don't know much about either John Graham-Cumming or Michael Gove personally. I do know that this is a long and, dare I say, rather rambling e-mail, which to me reads more like a lecture written to look good for a public audience than a sincere request for action by a government minister. Perhaps that is just my natural scepticisim talking -- I have no reason to believe that John actually meant it that way, and I have nothing against him based on his comments on HN -- but keep in mind that civil servants have finely tuned senses about such writing, because a lot of the people who send it are trying to set the minister up in one way or another.
A more practical problem is that the original e-mail contains almost no actionable content. The only specific detail is Raspberry Pi, which is not mentioned until the second half of the message and by the author's own description is not yet ready. Given how many doomed government IT projects surely get described as "close to completion" right up until they fail with a multi-million-pound write-off, it would hardly be surprising if no senior government figure wanted to be associated with something potentially toxic like that at this stage.
Even if the minister were willing to take a look, if it is indeed contrary to government policy to promote such specific details on a national basis, then there is little the responding civil servant can do to help except explain what the policy is and who might be able to help instead, which they did. Multi-level governments inherently set rules for which matters are to be handled at which levels, and it is futile to propose deviating from such fundamental rules in isolated cases like this.
I suspect John's intended point might have been more about the benefits of teaching kids to code in general, but I'm afraid that just doesn't come across from the message unless your audience is likely to read between the lines (see my comment about public audience above). In any case, while it may be a perfectly reasonable position to take, nothing in the e-mail suggests any specific action the minister could take to further that goal, so at best it is going to achieve a +1 in an "issues of interest" spreadsheet and a courtesy reply.
I do love the final comment, asking for a personal meeting with a secretary of state based on a quick e-mail, though. You've got to love someone with the chops to go for that right from the start. Maybe I just went to the wrong university... :-)