...an innocent by standard is more or less someone in the wrong place at the wrong time...
Oh, "innocent bystander", just a spelling difference - thanks.
...the purpose is we raise animals for the purpose of food, its shitty to think of but they serve a purpose... they help the population by feeding us...
So the purpose (raising animals for food) justifies the practice. It may not be pleasant, or even right ("its shitty to think of"), but you believe it's necessary. In other words, the ends justify the means. Vegetarians are trying to show that it's not as necessary as you might think.
Still, a fair point. On training day for an advocacy gig was shown a video interview of a medical researcher who worked on chimpanzees. He knew it was wrong, and said as much. He spent time with chimps. He could see that they were just like us in every way that matters. He said that even if what he did wasn't right, it was necessary. He was a "Dark Knight", doing what needed to be done, even if he was hated for it by the very people he saved. Don't know if his statement was correct - that is, if his work saved human lives. It might have been.
Essentially, this is similar to Vice President Dick Cheney's argument for torturing "enemy combatants". Most Americans disagreed that it be could justified, but there might be very rare or hypothetical cases in which some would change their minds. For example, if a bomb was about to go off and torturing a captured perpetrator might provide information that could defuse it in time.
Even so, that can hardly justify the torture of people (or research on chimps) as a general practice. Many argue that it can never be justified, even if it might save others. Research on great apes like chimps is now in steep decline,
banned in a number of jurisdictions (the Netherlands, New Zealand, the United Kingdom, Sweden, and Germany). In the US, in 2013, Congress passed
The Chimpanzee Health Improvement, Maintenance and Protection Act, which approved funding allowing for almost all of the apes owned by the federal government to live in a more natural group environment. The transfer is expected to take up to five years, at which point all but 50 chimpanzees will have been successfully "retired".
Getting back to animal agriculture, the practice might be similarly justified by some, at least in rare cases where a particular human population still needs it to survive. Believe most vegetarians wouldn't take issue with this, if only because there are still so many cases where this doesn't apply. It makes sense to concern ourselves with these cases - involving a far greater number of animals - first. Realistically, we'll probably never get to the more difficult cases. Like the other examples (torture of humans, research on chimps), even if animal agriculture can be justified in rare or hypothetical cases, it doesn't justify it universally, as a general practice.