There are two issues here, (1) is deploying to Cloud Endpoints, (2) is viewing your API in the Endpoints Management Portal.
For (1): It should work without scrubbing, I've successfully deployed protos that reference long running operations before. It's not clear how you compiled the descriptor, so we'd need more details. But Oscar's workaround works well if you don't mind the extra step.
(2) may be a known issue in the Endpoints Management Portal. I don't work on that piece of the product, but I've seen
various other posts about it in the past. As a workaround, you can try modifying the script Oscar provided to also scrub out
google/api/client.proto references.