I've just started playing Reunion as opposed to TC, so I don't know if the following applies (especially given the random seed involved in the game), so here goes:
Yep, you're stuck with the missiles. Load a game from before you did that.
In my evolution of the game, trading energy cells from Power Circle to anything in Argon Prime is fairly lucrative; Combining this with occasional ore and silicon wafer runs makes it a pretty solid earner.
Power from Queens Space to Kingdom End is also quite good.
If you're still using the M4 class ship that you get at the start and you're using a vanilla starting point (Argon race, M4 Buster ship) then trading space fuel from Herron's Nebula to the local trading station is VERY lucrative. If you get scanned, reload. If it runs out of resources, explore and support it.
I started out doing pretty much the above; space fuel got me enough cash for my first freighter, and casual power/ore/silicon runs around the Argon system got me the rest.