Every animal is part of the living force though, no animal should be killed for the benefit of others, they should of moved them or something.
It really depends on the risks associated with moving the creatures versus the death of a few dozen in the immediate vicinity. Presumably these creatures are not unique to that area, but represent a local pack that has migrated into the region and are causing trouble. Allowing them to live may very well have been the worst of two bad options, which is why the "put them down" option was taken.
I'm inclined to judge the Jedi for their handling of the Flesh Raiders and for ignoring the twi'leks but for the "put them down" quest... no so much.