Wow - that's a LOT of money for a neuter!!!
Bandit was neutered by our vet, and he did not need a cone. We also did not use onesies - he just didn't need to be treated any differently than normal. We did our best to keep him quiet for a couple of days (which did not work out nearly as well as we had hoped), but it's almost like he didn't even notice the stitches or the surgery. He licked at it a couple of time as it was healing (I think the hair growing back was a little itchy) but he never chewed at it or bothered the actual stitches. His were disolving, so I'm not sure when they were completely gone.
I have had several experiences with the low cost spay/neuter clinic in my area. I live on a creek, and for whatever reason that seems to attract people who seem to think it's the perfect dumping ground for their unwanted pets - I've rescued 8 week old pups from back there, all the way to a very old, barely able to move, nearly blind dog on one of the coldest and wetest days of the winter.
But I take them all in, clean them up, nurse them back to health when necessary, spay/neuter them, get them up to date on vaccines, then rehome (most of) them. So I've used the clinic many times over the past 5 or 6 years.
The main difference I've noticed is in bedside manner. By bedside manner, I mean the way they treat YOU not the way they treat the dogs! They all obviously care about the animals, but they aren't really concerned about establishing a long-term relationship with you (the owner), so they can sometimes be pretty abrupt and matter-of-fact with you. Not so much hand-holding and coddling you might get from your regular vet.
But the quality of care seems to be great, the surgeries have all gone extremely well, recovery time has all been just as quick as the animals I've taken to my own vet, and the docs all seem to be quite skilled - you really can't even see where the incision was when it's all healed (just like my own vet did it).
I know this is very long-winded, but I wanted to try and give you a little peace of mind. If you've been there and the facility looks clean, and the people you talk to seem to care about the animals, then I wouldn't hesitate at all.