I'm definitely not an expert on the matter, but I can tell you that when my wii was partial bricked (meaning I couldn't go into settings and get internet working) I googled around and found the only way to fix my problem was to put a new game in and update.
I hesitated for a while, since I too didn't want to risk losing my mods, but after about a week my need to get internet on the damn thing was too great so I updated using Drawn to Life.
The wii updated, it solved my brick problem. My homebrew channel remained, fully functional, as did my USB loader channel and my m player channel. Nothing at all had changed in fact, except that my wii now worked fine.
BUT! If you still don't want to risk it then you can use a loader like NEOGAMMA which let's you bypass the whole update thing anyway.