Попробуйте
delete(viper.Get("path.to.key").(map[string]interface{}), "key")
Пример:
[backends]
[backends.setibe]
[backends.setibe.servers]
[backends.setibe.servers.server0]
url = "http://192.168.1.20:80"
weight = 1
[backends.setibe.servers.server1]
url = "http://192.168.1.21:80"
weight = 1
Чтобы удалить "backends.setibe.servers.server1"
delete(viper.Get("backends.setibe.servers").(map[string]interface{}), "server2")