If you're concerned about the skill, etc., you can call several rescue groups and ask them about the reputation of the clinic.
Once upon a time, vets didn't spay anything under 6 months of age. Now they routinely do it within the first 3 months. You've had Rowdy for several months now - even if she is small for her age, she is unlikely to be small enough to create complications.
I disagree that there is a "high risk of cross contamination" at these clinics. Most are very careful about sterilization and separation of the cats. Can something happen? Yes. But that same thing can happen at a vet's office also. I've known hundreds of cats who have been spayed/neutered through these clinics over 30 years and have never seen one cat become ill from it. I have had one cat get spayed at a quality vet's office and become ill afterwards - in reality, the cat was already ill but not showing signs until the stress of the surgery. It would have happened no matter where she was spayed.
However, with that said, you have to go with your own gut feeling. There's no guilt with either choice you choose.