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I am sure many others have ran into the same issue, of needing to update jQuery for the frontend theme but not for the administration theme. Replacing jQuery site-wide can cause many problems. Surprised this feature was missing, I wrote a very simple patch that offers this functionality.
The patch provides a checkbox that allows you to ignore the admin theme. If ticked, it will not replace jQuery in the administration theme - making everything work as expected. I am sure this will solve a lot of headaches - or migraines...
Please let me know if you run into any issues or have questions. I am happy to help.