I know I'm too late to have my input considered with this update, but: Reading though what everyone else says here, warp containers sound like a "best solution" to remote mining (less cpu and energy cost/tick). The fact that they use energy, and decay costing energy seems overly complicated to upkeep (vs links with use energy and containers that decay).
I'd rather see structures that don't require creeps to preform tasks on them for them to do their job (like links, labs, terminals). Warp containers still require creeps to move their energy across room borders, and increase code complication but less cpu. If something like pipelines, that could pump less energy the bigger the system is, were introduced, I would think you'd see haulers and pipes depending on the situation (removing the best solution problem).
With respect to the terminal change, I'm not sure why civilians have to see the consequences. Just that same that structures can't be destroyed when hostile creeps are in your room, limit/block terminal calls.
An alternate suggestion to blocking terminals: Make mortars a thing. Essentially mini nukes that can be loaded up with different resources (where certain resources have different effects, just as boosts help your creeps, these will take away from enemy creeps). For instance if KH is loaded, it will reduce any creep/structure that has a .store property by some percentage.
I personally would like to see more inter-room actions, instead these updates would lessen inter-room actions (limiting terminals) and strengthen intra-room actions (with warp containers). lets see more things like mortars and pipes.
Also, I'd be interested in seeing what internal suggesting the dev team came up with even if they were considered too much of a change that they'd break peoples code.