An interesting warning. I have multiple answers, especially when it comes to STO. Two steps that can be taken to alleviate this effect:
1) Fewer Servers (like, maybe 1)
With space so large, it's really not inconceivable to populate space with a million player characters. The tech behind it may need to be tested out since that's unprecedented, but it hardly seems impossible, especially if common areas like Earth are large enough and content is progressively generate, eliminating the 'development time' barrier to massive servers.
2) NPC Fill-ins
Your crew is full of NPCs doing jobs meant for low level players. They're not as good as players, but they keep the ship together while you worry about the weightier matters of diplomacy and fleet organization. If there is a space that needs to be filled, let an NPC do a half job. In all of the above examples, suitable NPCs would have propped up the interdependent systems.
alternately:
3) Worry about it later
This is only a problem when the playerbase wanes. Until then, let the good times roll and just leave flexibility to implement the solution later.
I don't think a Trek game can really capture the Trek spirit without having interdependent systems. It's hardly a universe of soloers out there.