Yes you will have to maintain the mapping manually.
It is one time effort to load 1000 accounts in the rollup mapping rule.
If 1000 segment values could be loaded in a value set then they could also be loaded in the rollup mapping rule.
You can use data loaders. In fact you should use data loader in this case.
This is a pretty normal scenario and I dont see this as a big issue.
Mapping has to be maintained if you add new account values but that will be less frequent.