I think jalal bowing his head before kali mata is a way bigger deal than jodha being allowed to practice her religion. What he did in the temple was seen as idol worship, which is strictly forbidden in islam.
The feelings of the ulema on this whole issue of the hindu begum were probably building up this whole time and lastest incident of jalal bowing before a hindu god in a mandir was probably the last straw to break the camel's back. You have to remember that even though they were ulema and they were highly regarded, they couldn't just stand in front of jalal and openly rise against him for every small issue. It would have to be something major, which this definitely was.
Thankfully the letter from chrishti sahab came just on time to prevent the whole situation from turning into a disaster and jodha begum having to convert, so all ended well. However, I do think it was pretty stupid on hamida begum's part to rely on that to save jodha, when she had just blindly put her trust on her ammi jaan to save her.
I think the cv's are forgetting that communication in those days was very slow and all the letters would have to be delivered by road, through a messenger.