Sometimes happens that if you don't accomplish a mission, the enclave leaves the map or becomes enemy. Maybe in the meantime you are trying to escape from death or making something vital for your base.
I think that it could be a good idea to give an option to refuse the mission without losing partnership level (or a good probability to avoid to lose it), using influence points. In reality it could be a thing like "I'm sorry but we are doing this bla bla bla...". You will lose some reputation (influence) but neighbors can understand. This can open some intuitive gameplay options as
1 - Enclave personality: Neighbors can tend to understand (good attitude) or be demanding (bad attitude), by a hidden value
2 - Diplomacy (or a new) quirk skill - If you've a survivor with that skill, you'll lose less influence and improve the chances that they don't leave or become enemy.
In one of the last update it has been reduced the mission spawn rate. I think that managing the missions is better than reducing, because it improves the gameplay options, you can choose better what to so.