I do agree with this, and that the angle you're taking might not be the most novel/beneficial. You need to ask, what is the significance/impact of your research? What knowledge will be gained from it? Simply culturing and identifying the bacteria that grows in a ball python's mouth in order to educate the general public is perhaps noble, but ultimately fruitless. As you've pointed out with cats, and has been done with dogs, they harbor all kinds of pathogens in their mouths but the public either 1) ignores it or 2) takes it the wrong way. You'd be far better taking an approach to educate the public about microbiology and pathogens in general.
I don't think the research itself is uninteresting (see my previous post), but you need to frame it in a different context. Such as, what do we know about ball python digestion and immune systems? Given that they metabolize whole animals, this is a potentially interesting subject, and approaching an owner with that angle "I would like to investigate aspects of ball python digestion, here's what's known in the field ___blank___, here's what's not ___blank___, and here's what I would like to find out ___blank___." might get you a better reception than "I want to find out what's growing in their mouths." and sparking undue panic.
But, you need 1) a hypothesis 2) rationale 3) protocols 4) a way of analyzing and presenting the data in such a way that benefits the field without unduly scaring the general public (always a fun line to walk). As you've seen from the reactions here, most people are not going to be very accommodating of your approach. And while the owner's reaction to E.coli was perhaps....not grounded in science, he does have every right to refuse your request. It is your duty to convince/reassure people that your work is important, if they refuse, then you've most likely failed to do that.