That sounds like an interesting compromise, what other suggestions do you have for something like this?
I'd have an ability on shipyards (maybe unlockable?) which would disable/pause ship building while it deconstructs a selected ship, that way you have to balance building vs deconstruction. Not sure if you'd want to micro it on every ship - I wonder if there would be a way to multi-select ships in range, or order them to queue up for deconstruction... This would encourage having more worlds with shipyards to deconstruct ships, as in my playthoughts I don't build many shipyards at all.
Have the refunded resources be a % of the ship's initial value, which is further reduced by the % of the ship's health (so it can't be exploited as a way of getting around repairing ships by deconstruct > build new ones).