I think spaying is probably for the best. I also agree that because of her messed up cycles she's not a good canidate for breeding.
If you were considering letting her have the pups, I would think about what you'd do w/ the possible double merles. Really sight and hearing are the real issues, and aussie are more prone then some other breeds to eye problems in the double merles. The crazy part is when breeding merle to merle statistically 25% of the litter would be double merles, but I've seen litters w/ none and litters where most are double merle. In Iris's (my double merle) case out of 6 puppies, 4 were double merles! Thankfully only two had any issues (Iris being one). Many puppies are put down w/out waiting to see if they even have any issues. Personally if I wasn't prepared to find homes for every puppy (including the possibly deaf or blind ones) then I wouldn't go ahead w/ the pregnancy. I know it sounds like you already made up or mind, and I think that is for the best.
I took two dogs in to be spayed yesterday, they are great pyr mixes (sisters), one belongs to my dad and the other to my sister in law. Both had been in heat, one had just gone out. It turned out my dad's was pg (I was already pretty sure she was), she was probably pretty far along (since I could already tell), and I've felt really bad about it, part of me wishes they wouldn't tell me. But I know it was a very bad idea to let these unwanted puppies be born. I know I'm going to feel guilty for awhile, but I know it was for the best.