I have tried to get around this by creating a two step process. When considering whether or not to create a creature the first step is asking "Does it have humane values?" The second step is asking "Will it live a good life, without excessively harming others in the process?" If the answer to either of those questions is "no," then it is not good to create such a creature.

Now, it doesn't quite end there. If the benefits to others are sufficiently large then the goodness of creating a creature that fails the process may outweigh the badness of creating it. Creating an animal without humane values may still be good if such a creature provides companionship or service to a human, and the value of that outweighs the cost of caring for it. However, once such a creature is created we have a responsibility to include it in utility calculations along with everyone else. We have to make sure it lives a good life, unless there's some other highly pressing concern that outweighs it in our utility calculations.

Now, obviously creating a person with humane values who will not live a good life may still be a good thing as well, if they invent a new vaccine or something like that.

I think this process can avoid mandating we create viruses and mice, while also preserving our intuition that torturing cats is bad.

If you assign any positive utility at all, no matter how small, to creating happy low-complexity life, you end up having to create lots of happy viruses (they are happy when they can replicate).

You are using a rather expansive definition of "happy." I consider happiness to be a certain mental process that only occurs in the brains of sufficiently complex creatures. I consider it to not be synonymous with utility, which includes both happiness, and other desires people have.