I'm pretty sure Engi C only has that beam drone in order to take down Zoltan shields. Otherwise, it's rarely worth using alongside the starting weapons, in my opinion.
You must be using a different Engi C than me! Against something with a shield its doing a maximum of 1 damage per volley without the beam drone deployed, and that's assuming both shots hit. Even the early sectors, dealing damage at that rate is just going to give you hefty repair bills - at best. An early, extra weapon makes all the difference (as with every ship!), but hacking is a great alternative, well worth while with the beam drone (and the Defence Scrambler Augment
And in general, I like the beam drone over the combat drone, which misses too often to reliably take down a shield bubble.