Currently there no vehicles in Wagon R category (hatchback) to offers automatic in diesel. However, Maruti is planning to launch Celerio diesel this year and is most likely that the automaker will couple it with an AMT - Automated manual transmission. Moreover, like the Zest, Tata is also highly expected to launch Bolt with the F-Tronic AMT soon in diesel trims.
As you told, it was a free service and you just got the engine oil changed and wheel alignment. So, it should be lesser, however, ask for the type of engine oil as if they have used synthetic engine oil than the cost is justifiable.