I agree with getting the cystocentesis. It's the best way, the vet gets a nice clean sample. Once air hits the urine, it changes, there's nothing that can be done about that.
Just make sure your kitty has a full bladder when you take her in. You can do this by feeding her a watery meal (add water to some canned food, mix well) about an hour before her appointment, then put her in her carrier to keep her from using the litter box, until it's time to go to the vet.
I have a FLUTD cat, Mazy, who gets her urine checked annually (or more often if trouble is suspected) and, even though she can be a real terror when at the vet, she alllows the cystocentesis with just a little musical growling.
I also agree that a CRF kitty, unless UTIs are suspected should not need more than the one urinalysis. My CRF kitty, Ootay (rb 5/09) also had no trouble with the cystocentesis. She, also, had to have blood work every few months, until her last few months, I stopped the blood work, wanting her to just enjoy her last months without any extra stress.
(She also had megacolon, hyperthyroid disease, high blood pressure, arthritis, heart murmur and stroke.)
Are you giving Boo subq at home?