One effect of being tied to a shop may be insurance - from what I've seen, I'm paying a bunch less in insurance since we're covered by a shop group policy, instead of having to get my own. Depending on the number of certs/year it may or may not be a factor for you.
I guess I'm what I'd consider to be a "casual" instructor. I do it because it's a lot more fun that the day job, and for the most part I'm glad that I have a shop involved to deal with the overhead part - loaner/rental gear, sales of student personal gear, paying the pools we use, negotiating insurance, etc. I can focus on scheduling the students in way that's mutually agreeable, and spending time on actually teaching. I'm not trying to make a living off of it - right now I'm happy if it breaks even and buys me some new gear each year. I'm not spending a bunch of extra time out of my day-job day hustling for business.
As far as the Mares/SSI thing, I've never hear even rumor (from the shop side) of any such pressure. We sell a little Mares stuff, but our primary lines are the Huish things (Atomic/Zeagle/Bare/Oceanic/etc). There's some expectation that we'll be using what we sell during classes, but it's not a hard and fast rule, and there are discounts offered to make that easier, and use of shop gear too. I don't have to play salesman though, but in the event that I bring in a student on my own, I make a little more off the class for my trouble.
Big picture, the whole "tied to a shop" experience is going to depend on what shop you're working with - I don't think this will be different for any agency where you're in a situation where you're dependent on a shop for *something*. I'm sure that there are independent instructors out there who have been able to flip the script and be the ones bringing the business to the shop, but that's not for everyone. I don't want the hassle or liability of having student loaner gear, or having to put the student thru the hassle and expense of going somewhere to rent it, and get air fills and such. All of that gets baked into the course cost since it's the shop selling it. There was another discussion here recently about whether to charge friends and family or not for instruction. I can waive my fees if I want, but the shop is still going to charge their part which covers gear/air/pool/course-material/etc - as well as the perqs afforded to any assistants that might be helping me. Takes the pressure off of me to do anything for 'free' even if I am foregoing my income on the class, if that makes sense.