A few points. One, the construction of animal shelters is not the goal of animal liberation. Congested animal shelters are a result of human indifference to animal suffering, whether through the damaging opinion that animals aren't capable of critical thought (they are), or through the damaging industry of pet breeding. So colluding animal liberation with literally putting them in orphanages seems like misguided reasoning, and a misinterpretation of the end goal.
Two, yes, I concur that we should stop being invasive on naturally occuring processes, and animal liberationists would always tend to agree with you. The constructs that create animal suffering are mechanisms of capitalist consumption (state, private, or otherwise). If profit motive, national glory, and general growth-obsession was taken out of the equation, we would have no need to slaughter animals en masse, plow the rainforest for industrial farm space, etc.
I assure you, one of the main incentives for veganism is not that we believe eating animals is wrong, it's that eating meat necessitates living in an uncanny, disconnected world of needless suffering and environmental horror.