Oops, you're certainly right here, yep. Operators can't use a terminal if the 'T' section is destroyed, but I must've forgotten to check whether the terminal was actually operational!
And this brings to light a pretty cool tactic with another trade off--since destroying an Operator before it reaches a Terminal can be difficult, if you're willing to give up the Terminal itself you can just shoot it if you have a clear shot, since they're much easier to hit and disable.
This'll be fixed next release.