My issue doesn't apply to this game since it has no limits on how many pets you can "destroy".

The other game I am playing I am exceedingly close to the finish of my project. What should I do with my less than perfect pets? I don't want to throw them in the pound where any one can grab a pet for free and then use my pets to breed even more perfects and destroy my months of work.

We do have something called the State Portal Service Branch that will "destroy" the pets but you are limited to only 5 pets per day and since I breed often and in large groups, I would never catch up.

I could sell them but the issue arrises again that they would take my high traited pets and breed their own. How do I protect my breeding lines and still keep space in my stables to continue my breeding projects?

I play beastkeeper too, and perhaps you should sell them for a very high price. Or aternatively ask a very trusted player to take them and destroy them for you.

unfortunately beastkeeper does not have a very talkative community so I have very few friends... and only 1-2 that i speak to on a semi regular basis