8 years ago we adopted our first dog, a husky malamute from the SPCA. She was 8 years old at the time. What a great dog. And I wasn't allergic to it. So 6 mos after her passing we've found another husky. This time, a 6 week old puppy.
Yes, we got her a little early, but the mom was under duress.

Now for the challenge. We've got an 18 y.o. cat who we also adore. The puppy came from a breeder, but had giardia from a dog that visited the property. We could have returned her, but fell in love.  The breeder did have her on antibiotics, but this stuff is a challenge to kill.  She is on her second batch of anitbiotics over the 2 weeks we've had her.

We have built a pen area with baby gates in our kitchen, we use training pads, plus we take her outside 3-4 times a day. We keep her and our cat away from each other. When she cries during the night my wife will sleep with her on the couch, because she is so young. But now we're trying to break her of the crying habit.

We can't give her more freedom until the giardia comes back negative. Should we start ignoring her cries at night? Helppppppp.
And should we continue to get up and change the training pads in the night because of the giardia? She only poops and pees on the pad when she's in the house. (She uses the great outdoors when we have her out).

Should we not sleep on the couch with her at night, even though it may just be for a couple of hours?

I can tell you what I did for my two puppies (bought a year apart) but its not advice per say, its more my...experience my breeder btw, recommended the complete opposite. But...I DID sleep near the puppy in their first week or so (on the floor, right next to the crate to be exact) and from what I can tell, my dogs suffered no ill affects from it. Its said that the sooner the puppy learns to be by itself, the better, and that by coddling the puppy by sleeping near it when its young can help create seperation anxiety, but in my experience, that has never happened, and Ive owned several ( 4 Huskies and 1 Malamute) in my life and I did it with atleast 3 of them (5 including my current two). In my mind, the puppy is already stressed enough in its first few days or so and any way I can relieve any of it, I will do it. Again, this isnt advice, only my experiences and someone else may chime in with a totally different recommendation.

As far as the Giardia is concerned, with you using training pads you will not only want to change the training pad but wipe her feet off. If she is standing on that pad after she messes on it then she can be reinfecting herself if her feet aren't being cleaned off. My mutt had giardia when we got him from a shelter and I kept lysol wipes on hand. When he went outside, his feet got wiped off before he came back inside. Wherever he pooped outside the excrement was scooped up and disposed of where neither he nor another dog would be able to get to it and I was even going as far as bleaching the spots where the poop landed. I had him and my husky at the time and managed to allow them to live together in the same house, ride in the same car, and play together without ever getting my other dog infected. He was cleared within the first round of treatment.

Thank you TwisterII and Artic_Wind for your replies!