The logic is not that it results soleley from factory farm conditions. It's that factory farm conditions are ideal for the exchanging of genetic material that leads to these new viruses. I.E. they don't HAVE to come from factory farms, factory farms make it more likely that they will come about and accelerate their evolution into new and more virulent forms.
I think the "conspiracy" aspect comes in when the dangers are exagerrated to (a) get people panicky which is always useful to the system (easier to manipulate people's emotions); (b) to sell their Tamiflu, useless face masks, etc etc; and possibly (c) once they've created enough of a panic, to (for example) ban all public gatherings, thus preventing people taking to the streets and protesting etc. I don't think the actual outbreak of the disease is the result of any conspiracy. It could be I suppose but where's the evidence for it? A lot of times the simplest explanation for something is the right one, or so it seems to me anyway.