Update: I tried a simple File -> Import Records -> File... and it crashed when trying to open the excel file. So it has nothing to do with the SQL Server table.
I then opened the file in excel, and saved as itself. I then retried File -> Import Records -> File... and it did not crash.
I think I will write a powershell script that saves the excel file as itself prior to running the import. I'm still curious as to why FileMaker would crash though.