Linux-firmware is the only one I would try. Definitely don’t try the kernel* packages. Microcode_ctl has spectre/meltdown fixes for Intel CPU. You can remove it if you have AMD CPU, but there should be a similar package for that which will probably have the same issue. A lot of the qubes-packages sound important too. If that tool is just looking at the license, you should reconsider. Stallman is really picky about licensing.
I strongly recommend against removing any packages from a minimal template, since it’s already minimal. Doing so will almost certainly break things. If you want to know which packages you can remove from a non-minimal template, you should probably just take the opposite approach instead: Start with a minimal template and add only the packages you want.
I disagree. Of course you should never remove anything when you don’t know what you are doing, but, for example, if your hardware supports FLOSS, you should be able to remove every proprietary firmware without any negative consequences.