I agree this seems fixable in so many ways aside from simply taking it away, that whatever reason they come up with is just hollow excuses/misdirection.
They could gate it so it's say 1 per month per account or something, that would stop (or severely limit) the exploiting. They could flag the dilithium as untradable. They could withhold the award until you reached a certain level, or meter it out as you level (10,000 at spawn, 10,000 at Lt Cmdr, etc). so you couldn't just spam new characters and then shuffle the dilithium off via the exchange, etc.
It's just that taking it away for everyone is the easy/lazy way out since it requires little to no programming, and it also furthers their goal of controlling the economy, creating a scarcity of dilithium so people pay in the Cstore to hop on the currency exchange. Convenient that.