In most circumstances, I'd be using the magnifier too. It's there to help you achieve critical focus. If I'm not using the magnifier, I've usually either pre-focused or stopped down a bit (e.g., f/5.6 or f/8).
If you usually wear glasses, you could consider replacing the standard dioptre on the WLF with one with more correction? Ffordes have a few for the waist level finder, but there appear to be a bunch on eBay if you search
Bronica eye correction:
http://ffordes.com/category/Medium_Format/Bronica/Bronica_SQ/SQ_Accessories
For some types of photographs, the tripod will help immensely. For others, it might not. Certainly, the clinically sharpest photos will be obtained from a tripod using mirror lock up, but that isn't always wanted, desirable, or even possible.
I used to shoot 95% of my Bronica photographs handheld, but the tripod has received much more use over the last year. I've had a lot of practice though, so I'm quite comfortable either way.
Maybe consider purchasing the speed grip? I've been using mine a lot lately.