Absolutely you should not have him circed to prevent harm to the foreskin --- because circumcision will be far worse!
Mama, deep cleansing breaths first of all.
You did the right thing by keeping him intact and you have not failed to protect him -- you weren't as educated as you are now even a week ago about the intact penis, and by the time you finish educating yourself here and with the resources you have, you will know MORE than the ignorant health care professionals about the intact penis.
First things first: you should not go forward with this procedure until you are guaranteed that they will not retract him again.
There's nothing life-threatening going on, right? I assume if this were life-threatening he'd be in the hospital right now. So you do have a little time to reschedule if necessary and educate yourself and figure out what your options are.
Here is the deal about the intact penis -- it is not a germ-ridden ticking time bomb. The infant foreskin is sealed to the glans by synechial tissue, the exact same type of tissue that bonds your fingernails to your nailbeds. This is precisely so pathogens will not enter the preputial space (the space between the foreskin, or prepuce, and the glans (head) where the urethra opens (meatus)).
So retraction is simply not necessary to avoid "germs" because the foreskin itself keeps harmful germs out of the urinary tract. The sphincter at the end of the foreskin opens to allow urine out upon urination, and closes up again to seal the penis off and protect the urethra.
Assuming your son is breastfed, and assuming he was born vaginally, he's colonized with beneficial bacteria from you and from your breastmilk and those beneficial bacteria as well as the other protective components of breastmilk do more to protect him from a urinary tract infection than anything else.
In an intact man who's fully retractable, because the synechial tissue has broken down allowing separation of the foreskin from the glans, a "clean catch" urine sample or a catheterization would require at least partial retraction to allow cleaning of the glans, but it doesn't require scrubbing like you'd prep for surgery -- just cleansing like you'd do on a woman before doing a clean catch or cath.
But on an intact boy, there's simply no space for germs to inhabit any more than germs live between your attached fingernail (the pink part) and your nail bed. There's no open space for them to get in there.
Premature retraction is like ripping the fingernail off the nailbed. It's harmful and unnecessary -- you don't need to rip your fingernails entirely off to clean underneath the detached part of the nail, and you don't need to retract the entire foreskin to get a catheter into the intact penis.
An educated and informed health care provider should know about the intact penis and the harms of premature retraction, and you should not let them bully or cow you into accepting out-of-date, uninformed, and harmful medical procedures. They don't know what they're talking about if they say full retraction is necessary, and you should calmly -- calmly but firmly -- insist that they do it your way, because that's the way they do it in every other medically advanced society where the intact penis is the norm.
I would contact Marilyn Milos at www.nocirc.org
and John Geisheker or George Denniston at www.doctorsopposingcircumcision.org
and see what resources they have for you in terms of finding another provider or better hospital, and educating these people on the harms of premature retraction.
Hang in there -- remember, stay calm but firm! You are not crazy, or anxious -- you are smart and educated.