Not at all. The difference is that meat eaters are not doing the killing. They are eating dead flesh, they are not taking the life of sentient beings. The transformation from sentient being to dead flesh has been carried out by someone else, that is their kamma, not the meat eaters. By taking antibiotics or worming medicine you are directly doing the killing of a living being.
Although not canonical, the background story to the first verse of the dhammapada has a blind arahant doing walking meditation. He kills some insects because he couldn’t see them and in the morning other monks having seen the blood (haemocoel I guess), complain to the Buddha that the monk has committed the offence of killing. The Buddha explains that it was unintentional because he could not see them. The implication is that had the monk not been blind, saw the ants, and stood on them regardless it would be intentional. This was my reasoning.
I have some thoughts on veganism in this thread: The Dhamma and Veganism/Vegetarianism