Find out if you can make your query run faster. Optimize it or add indexes. In the web page, display a progress bar and show a message that the query will take x minutes so the user doesn't give up and think the page hang. Let them know the expectations.

Compiling shouldn't be hard. Load the source in VS, make the change, compile and upload the assemblies or just upload the affected assembly, if both source and production are the same version.