Have I got the situation right? You have a gold card season and are attempting to travel with your son on a journey fully covered by your gold card? I can see the frustration here. If there was another adult travelling then you could select the gold card rate for both adult and accompanying child(ren). I guess that in the majority of cases it will be a season ticket holder travelling with partner and child(ren). Your situation may be relatively unusual, but in this day and age it is becoming more common, for a multitude of reasons.
The problem from the TOCs point of view is that to make the £2 child ticket available on it's own from a machine would drastically reduce the revenue they collect. There isn't an easy way around this, short of changing the programming of the machine to somehow read the gold card ticket to validate issuing a stand-alone child ticket. It doesn't even seem possible to purchase this ticket online. When bought from a human (either ticket office or guard) the validity of the gold card can be checked.
To answer your original question, I would indeed be inclined to write. I wouldn't necessarily phrase it as a complaint, as such. But it is valid to ask if they agree that it is inconvenient not to be able to purchase the required tickets when the ticket office is closed, and is this really how they reward passengers who pay upfront for a year. Even suggest that the inconvenience makes you wonder whether it's worth travelling by train. If you make the letter as constructive as possible then it may at least cause the senior management to think. Indeed if you don't get at least a sympathetic response from customer services, acknowledging your situation, I would then write direct to the man at the top.
I would stress though that you shouldn't feel any worry or nervousness about travelling without a ticket for your son. If there is no open ticket office then there genuinely is no opportunity to buy. You absolutely are entitled to travel and pay on board or at the end.